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U.S. Fish & Wildlife Service Houghton Dam Removal Environmental Assessment Sand Lake National Wildlife Refuge
Houghton Dam Removal Project Environmental Assessment
Contents
Introduction ..........................................................................................................................1
Proposed Action ............................................................................................................................... 1
Background ...................................................................................................................................... 1
Purpose and Need for the Proposed Action ............................................................................5
Alternatives ...........................................................................................................................5
Identified Dam Deficiencies ............................................................................................................. 6
Alternative A – Remove and Breach the Service Spillway (Proposed Action) ................................. 6
Alternative B – No Action Alternative .............................................................................................. 7
Alternatives Considered, but Dismissed from Further Consideration ............................................. 7
Affected Environment and Environmental Consequences of the Action ................................... 9
Resources Dismissed from Detailed Analysis................................................................................. 10
Resources Carried Forward ............................................................................................................ 11
Summary of Analysis ...................................................................................................................... 26
Mitigation Measures and Conditions............................................................................................. 27
List of Sources, Agencies, and Persons Consulted .................................................................. 28
List of Preparers ................................................................................................................... 28
Public Outreach ................................................................................................................... 29
References........................................................................................................................... 29
Tables
Table 1. Federally threatened, endangered, and candidate species and state special status
species potentially found in the project area or potentially affected by the project. ............ 12
Table 2. Additional sensitive bird species known to occur at the Refuge. .................................... 17
Table 3. Effects on resources from the Proposed Action. ............................................................. 27
Figures
Figure 1. Vicinity Map ...................................................................................................................... 3
Figure 2. Proposed Action ................................................................................................................ 4
Figure 3. Conceptual Dam Plan View and Breach Structure ............................................................ 8
Appendices
Appendix 1 Public Notice
i
Houghton Dam Removal Project Environmental Assessment
[page intentionally left blank]
ii
Draft Environmental Assessment for
Houghton Dam Removal – Sand Lake National Wildlife Refuge
April 2021
Introduction
This Environmental Assessment (EA) is being prepared to evaluate the effects associated with the
proposed action and complies with the National Environmental Policy Act (NEPA) in accordance with
Council on Environmental Quality regulations (40 Code of Federal Regulations (CFR) 1500-1509) and
Department of the Interior (43 CFR 46; 516 Department Manual (DM) 8) and U.S. Fish and Wildlife
Service (Service) (550 FW] 3) regulations and policies. NEPA requires examination of the effects of
proposed actions on the natural and human environment.
Proposed Action
The Service is proposing to safely remove the existing service spillway structure of Houghton Dam,
which is located on the Sand Lake National Wildlife Refuge (Refuge) in South Dakota. The existing
structure has severely deteriorated over the years and due to recent flood events has been overtopped
several times. Due to the minimal use and impact of the structure, the Service has determined that
instead of a replacement or repair, it would be more appropriate to demolish and remove the existing
structure and increase the opening to return the James River to more natural flows. Removal of this
structure would include removing the 110-foot existing concrete structure and increasing the breach
with an additional 40 feet, for a total breach width of 150 feet. The Proposed Action is described in
greater detail below.
A proposed action is often iterative and may evolve during the NEPA process as the lead agency refines
its proposal and gathers feedback from the public, tribes, and other agencies. Therefore, the final
proposed action may be different from the original. The Proposed Action for this project will be finalized
at the conclusion of the public comment period for the EA.
Background
National wildlife refuges are guided by the mission and goals of the National Wildlife Refuge System
(NWRS), the purposes of an individual refuge, Service policy, and laws and international treaties.
Relevant guidance includes the National Wildlife Refuge System Administration Act of 1966, as amended
by the National Wildlife Refuge System Improvement Act of 1997 (16 United States Code (USC) 668dd et
seq.) (NWRSAA); the Refuge Recreation Act of 1962, and selected portions of the CFR and Fish and
Wildlife Service Manual.
The Refuge was established pursuant to the following legislation:
• Executive Order (EO) 7169 (September 4, 1935) (“…as a refuge and breeding ground for
migratory birds and other wildlife…”)
1Houghton Dam Removal Project Environmental Assessment
• Migratory Bird Conservation Act
• Fish and Wildlife Act
• NWRSAA
• Refuge Recreation Act
The mission of the NWRS, as outlined by the NWRSAA, as amended by the National Wildlife Refuge
System Improvement Act (16 USC 668dd et seq.), is to:
“... to administer a national network of lands and waters for the conservation, management
and, where appropriate, restoration of the fish, wildlife, and plant resources and their habitats
within the United States for the benefit of present and future generations of Americans”
The Refuge was established in the mid-1930s as a refuge and breeding ground for migratory birds and
other wildlife. The 21,498-acre Refuge lies in the James River basin in Brown County, South Dakota. This
northeastern area of South Dakota is in the heart of the prairie–pothole region of the northern Great
Plains and plays a major role for migratory birds.
Houghton Dam was constructed in the 1930s by the Civilian Conservation Corps and is currently
classified as a small-sized, low-hazard-potential dam that was built across the James River to impound
and enhance Mud Lake. The current embankment dam is owned and operated by the Service and is
located on the Refuge (Figure 1). The purpose of the existing structure is to impound the nearly 5,300
acres of Mud Lake, which provides habitat to more than 48 species of mammals and 60 species of fish.
Houghton Dam is an approximately 6,400-lineal-foot earth embankment with a 110-foot-long water
control structure that serves as the service spillway. Currently, the stoplog service spillway and bridge
needs replacement. A bridge inspection completed in 2018 had indicated that the guard rails are
considered unsafe and that the existing structure has significant concrete cracking and spalling on the
bridge deck as well as on the support walls. Additionally, the existing structure does not allow for
floating debris to pass through it, resulting in large masses of debris piling up and restricting the flow
through the structure. The current water control structure creates a hazardous condition when Refuge
staff must remove the stoplogs. With the debris accumulation, Refuge staff cannot remove the stoplogs
from the crest of the spillway and must climb down in front of the structure to remove them.
Furthermore, high river levels in 2019 have overtopped the dam several times, resulting in extensive
damage to the existing embankment. The existing dam was renovated approximately 8 years ago and
due to the dam overtopping from significant wet seasons, that entire investment has been virtually lost.
In 2018, the Service developed a plan to replace the existing Mud Lake water control structure to allow
for reliable, safe, and more accurate water management on the upper pools in the Refuge. The designed
construction cost to remove and replace the existing water control structure was approximately $1.2
million. Based on the significant construction cost for a water control structure that will continue to see
overtopping in the future, the Service decided to evaluate the potential for breaching the existing
structure as a viable alternative to a complete replacement. Figure 2 shows the project area with the
Proposed Action.
2Houghton Dam Removal Project Environmental Assessment
Figure 1. Vicinity Map
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Figure 2. Proposed Action
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Purpose and Need for the Proposed Action
The purpose of the project is to address current and future dam safety concerns and associated public
safety risk, restore the river basin to more natural flows, and maximize migratory bird and other wildlife
habitat in keeping with the purpose of the Refuge.
The need for the project includes the following:
• Minimize future dam safety concerns;
• Help restore the river basin to more natural flows;
• Reduce future operational and maintenance costs that have been incurred from overtopping
during weather events;
• Create potential habitat for birds;
• Minimize public safety risk and minimize safety concerns for Refuge staff performing
maintenance of the existing structure; and
• Allow Mud Lake to maintain management capabilities with self-control.
In addition, the Refuge must fulfill the Service’s priorities and mandates as outlined by the NWRSAA (16
USC 668dd(a)(4)) to:
• Provide for the conservation of fish, wildlife, and plants, and their habitats within the NWRS;
• Ensure that the biological integrity, diversity, and environmental health of the NWRS are
maintained for the benefit of present and future generations of Americans;
• Ensure that the mission of the NWRS described at 16 USC 668dd(a)(2) and the purposes of each
refuge are carried out; and
• Assist in the maintenance of adequate water quantity and water quality to fulfill the mission of
the NWRS and the purposes of each refuge.
Alternatives
The Houghton Dam Removal Alternatives Assessment Report was completed in spring 2020 (Wheeler
2020a). The report identified dam deficiencies, summarized five conceptual alternative plans, evaluated
those alternatives, and identified a selected alternative that was recommended to best address the dam
deficiencies and reduce the risk at Houghton Dam. The alternatives were evaluated based on the ability
to adequately address the dam safety issues, calculate construction and long-term operational cost
savings, identify the ability to maintain or restore the river basin, assess the ability to create additional
wildlife habitat, and analyze the impacts on public safety.
Of those alternatives evaluated in the report (Wheeler 2020a), the Service is proposing the
following alternatives to respond to the identified dam deficiencies described below, and the
purpose and need of the project. Alternative A, the Proposed Action, is to demolish and remove
the existing structure and increase the opening to return the James River to more natural flows.
Alternative B is the No Action Alternative. The two alternatives are described below.
5Houghton Dam Removal Project Environmental Assessment
Three other alternatives were developed and evaluated by the Service in the Alternatives
Assessment Report (Wheeler 2020a). After evaluating the five alternatives to mitigate the dam
safety issues and current deficiencies at Houghton Dam, these three alternatives were not
carried forward for detailed analysis. Detailed descriptions of all five alternatives, field
investigations, and evaluation criteria are available in the Alternatives Assessment Report
(Wheeler 2020a).
Identified Dam Deficiencies
The Service identified several deficiencies at Houghton Dam in the Alternatives Assessment Report
(Wheeler 2020a), which are summarized below.
The spillway is undersized to pass the Inflow Design Flood (IDF)
The existing service spillway has a normal freeboard of approximately 3.67 feet (from the dam crest to
the normal pool) and is capable of passing approximately 2,000 cubic feet per second (cfs) before
embankment overtopping is expected to occur, which is less than the 5-year flood (Wheeler 2020a). The
IDF for Houghton Dam, a low-hazard-potential dam, is the 100-year flood with a peak inflow of 13,000
cfs (Wheeler 2020b). The existing spillway can only pass approximately 15 percent of the IDF prior to
embankment overtopping occurring.
The existing concrete structure has significant deterioration
The concrete bridge and spillway structure have signs of significant concrete deterioration. This
deterioration was documented in a 2018 bridge inspection (Wheeler 2020a), and repairs have not been
made.
The dam is experiencing a significant amount of uncontrolled embankment overtopping due
to the significant flooding
High river levels experienced in 2019 resulted in the dam being overtopped. These overtopping events
impacted the embankment stability and resulted in erosion along the crest and the downstream
embankment. The damage led to the subsequent closure of the auto tour route.
There are concerns associated with increasing sedimentation in the reservoir
The U.S. Geological Survey (USGS) completed a sedimentation study in 2003, indicating that Mud Lake is
continuing to experience sedimentation increases due to the surrounding agricultural lands and deposits
in the reservoir.
Alternative A – Remove and Breach the Service Spillway (Proposed Action)
For the Proposed Action, the existing service spillway would be removed. Due to the minimal use and
impact of the structure, the Service has determined that instead of a replacement repair, it would be
more appropriate to demolish and remove the existing structure and increase the opening to return the
James River to more natural flows. Removal of the structure would include removing the 110-foot
existing concrete structure and increasing the breach with an additional 40 feet, for a total breach width
of 150 feet. Construction will include the use of temporary water barriers to control and divert reservoir
inflows to provide a safe and dry working area. The removal construction will consist of saw cutting and
6Houghton Dam Removal Project Environmental Assessment
removing the existing concrete structure. It is anticipated that the existing concrete apron will remain in
place as a permanent feature. Contractors will use large excavation equipment to excavate and dispose
of the additional 40 feet of embankment to be removed to complete the channel opening. Imported
riprap will be installed on the excavated slopes to provide stability and limit future erosion during
significant river inflows. This dam breach would mitigate the dam safety deficiencies by removing the
inventory status of the dam. The James River would be free to flow naturally through the spillway
breach, and reservoir pool levels would be controlled by Columbia Dam operations.
This single breach alternative would eliminate any future maintenance required with the service spillway
structure. The main feature of this alternative would be to remove the existing reservoir control
structure at Houghton Dam and return flows to the natural channel. The breach would be lined with
riprap bedding and riprap protection to limit any potential scour and erosion. The conceptual dam plan
view and breach section for construction of the Proposed Action is shown on Figure 3.
The projected construction schedule is approximately three months and would likely occur in late
summer and early fall (2021), when the James River is at historically lower flows.
The Proposed Action has been selected by the Service as the preferred alternative for the following
reasons:
1. This alternative declassifies and reduces the regulatory requirements to maintain the dam;
2. The overall construction cost for this alternative is significantly less than other alternatives
dismissed (discussed below); and
3. This alternative reduces long-term maintenance costs associated with the existing structure.
Alternative B – No Action Alternative
Under the No Action Alternative, the Refuge would continue to expend labor hours and expense on
general maintenance of the dam and repair of the auto tour route. This alternative would not result in
modifications or significant repairs to the existing structure beyond any general maintenance and would
not address the deficiencies of the existing spillway or any of the other identified deficiencies. In
addition, the dam would continue to overtop during severe weather events. Public safety and personal
property would continue to be at risk during maintenance of the dam and auto tour route.
Alternatives Considered, but Dismissed from Further Consideration
Replace Existing Service Spillway
This alternative would consist of removing the existing deteriorated service spillway structure and
replacing both the spillway structure and vehicle access bridge for the auto tour route. This alternative
was dismissed from further consideration as the alternative would only address the deficiencies of the
existing spillway structure by replacing the structure in-kind. It would not address dam safety
deficiencies and long-term maintenance issues.
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Figure 3. Conceptual Dam Plan View and Breach Structure
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Address the Dam Safety Deficiencies
This alternative would consist of raising the dam crest elevation approximately 2.5 feet to an elevation
of 1,294.7 feet, lowering the emergency spillway crest near the left abutment to an elevation of
1,288.52 feet, and replacing the existing service spillway. This alternative would address the dam safety
deficiencies and make Houghton Dam a jurisdictional low hazard dam capable of passing the 100-year
inflow without overtopping. This alternative was dismissed from further consideration because of the
expected maintenance issues associated with meeting the required Service qualifications for a low
hazard dam, which include costs to raise and enlarge the dam.
Multiple Breach Locations
This alternative would remove and breach the existing service spillway structure as well as widen and
lower the left abutment spillway area to create two effective breach locations. This alternative was
dismissed from further consideration as it does not provide any additional benefit beyond the Proposed
Action and would be more costly to breach an additional location.
Affected Environment and Environmental Consequences of the Action
The Refuge was established in 1935 as a refuge and breeding ground for migratory birds and other
wildlife. The Refuge consists of approximately 21,820 acres in Brown County, South Dakota (Figure 1).
The Refuge manages the Sand Lake Wetland Management District, which contains 162 waterfowl
production areas. This entire area is known as the Sand Lake National Wildlife Refuge complex. The
marshes and open water impoundments of the Refuge are surrounded by prairie grasslands, cultivated
fields, and scattered woodlands along the James River. The Refuge was formed primarily from farms and
homesteads that failed during the drought of the 1930s. The project area is located along the auto tour
route and spans the James River. The dam was built to impound Mud Lake (see Figure 2 of the general
area and proposed project site on the Refuge).
This section provides brief descriptions of each resource affected by the Proposed Action. For more
information regarding the affected environment, please see Chapter 3 of the Refuge’s Comprehensive
Conservation Plan (Service 2005).
This section also analyzes the environmental consequences of the Proposed Action on each affected
resource. This EA includes the written analyses of the environmental consequences on a resource only
when the impacts on that resource could be more than negligible and therefore considered an “affected
resource” or are otherwise considered important as related to the Proposed Action. Any resources that
would not be more than negligibly impacted by the Proposed Action and have been identified as not
otherwise important as related to the Proposed Action have been dismissed from further analyses and
are described in the following Resources Dismissed from Detailed Analysis section.
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Resources Dismissed from Detailed Analysis
Water Resources
Houghton Dam is located on the James River, which is a mainstem river with constant flow. The Refuge
must use, maintain, and protect its water rights for the use of James River water. Refuge management
strategies are impacted by the extremely low gradient of the James River in northern South Dakota. The
upper James River is a unique portion of the total James River ecosystem in South Dakota. At the
Refuge, the flow of the sluggish James River is interrupted by two natural pools (Mud and Sand Lakes)
that have been regulated by low earthen dams and water control structures. Both lakes are shallow;
Mud Lake averages about 1.5 feet deep and Sand Lake averages about 2.75 feet deep with current
management. The maximum depths of the lakes are approximately 6 feet. Margins and other shallow
areas of both impoundments produce dense stands of emergent vegetation.
Water levels are manipulated on Mud and Sand Lakes and five subimpoundments to modify emergent
vegetation to help meet wetland objectives. During the nesting period, the Refuge attempts to hold
water levels steady to protect the nests of colonial, overwater-nesting birds. The critical period is May
15 through August 1, during which sudden changes place nesters at risk.
As described in the Land Use section, the Proposed Action would result in minimal differences between
the existing conditions and proposed conditions because of the downstream restrictions at State Road
10, which is immediately downstream of Houghton Dam. No adverse impacts on water resources would
be anticipated within the project area and upstream and downstream of Houghton Dam after the dam is
decommissioned.
In addition, Mud Lake is continuing to experience sedimentation increases due to the surrounding
agricultural lands and deposits in the reservoir (USGS 2003). However, the Proposed Action would not
provide a significant reduction in the sedimentation issues associated with Mud Lake due to the
downstream constriction at State Road 10 and Columbia Dam. The downstream restrictions limit water
surface head and velocity through the river system, which is needed to flush sediments downstream.
Because there would be negligible impacts on project area and upstream and downstream water
resources from the Proposed Action, this resource was dismissed from detailed analysis.
Socioeconomic Resources and Environmental Justice
The Refuge is in Brown County, South Dakota. Aberdeen, the third largest city in South Dakota, is the
county seat and the center of commerce for the region. The 2000 census estimated Brown County’s
population at 38,839 (U.S. Census Bureau 2019). Approximately 70 percent of the county’s residents
reside in Aberdeen. The Refuge lies about 40 miles northeast of Aberdeen.
The 2010 census reported the following population statistics for the county (U.S. Census Bureau 2019):
• 89.0 percent are white persons not of Hispanic/Latino origin
• 3.4 percent are American Indian and Alaska Native persons
• 3.6 percent are persons of Hispanic or Latino origin
10Houghton Dam Removal Project Environmental Assessment
• 2.8 percent are Asian persons
• 2.4 percent are Black or African American persons
In 2019, 80.2 percent of county jobs were in private wage and salary employment (people who work for
someone else) as compared to 76.6 percent for South Dakota (U.S. Census Bureau 2019). According to
the Data USA website (2019), the major employers in Aberdeen are office and administrative, health
services, education, manufacturing, hotel reservations, agriculture, higher education, the call center,
and support services.
Current Refuge staffing and budgeting generates 13 permanent and 4 temporary and seasonal
employees. The current staff accounted for an annual payroll, including salaries and benefits, of
$910,600 in 2003. In addition to providing salaries and benefits, the Refuge purchased goods and
services totaling $165,200 in 2003, approximately 65 percent of which was spent locally in the Brown
County economy.
There would be no local or regional impacts on socioeconomic resources from the Proposed Action as
the dam is not an attraction for the Refuge or region. In addition, there would be no local or regional
impacts on minority or low-income populations for the same reason. For these reasons, socioeconomic
resources and environmental justice were dismissed from detailed analysis.
Recreation Resources
Recreation resources within the Refuge are briefly discussed in the Land Use section. Houghton Dam is
not currently used for recreation by the public. For this reason, recreation resources was dismissed from
detailed analysis.
Resources Carried Forward
Wildlife Resources
Relevant Laws and Acts
Projects involving a federal nexus must comply with federal and state laws and regulations protecting
wildlife species including:
• Endangered Species Act of 1973, as amended (ESA; 16 USC §1531 et seq.)
• Fish and Wildlife Coordination Act of 1934, as amended (16 USC §661-667e)
• Migratory Bird Treaty Act of 1918, as amended (MBTA; 16 USC §703-712)
• EO 13186 Responsibilities of Federal Agencies to Protect Migratory Birds
• Bald and Golden Eagle Protection Act of 1940, as amended (16 USC §668-668d)
Federally listed threatened and endangered species are protected under the ESA. Potential effects from
a project on a federally listed species or its habitat resulting from a project with a federal action require
consultation with the Service under Section 7 of the ESA. Modification of designated critical habitat for a
federally listed species also requires consultation with the Service.
11Houghton Dam Removal Project Environmental Assessment
The Fish and Wildlife Coordination Act requires the federal action agency to consult with the Service and
state wildlife agency on issues related to conservation of wildlife resources for federal projects resulting
in modifications to waters or channels of a water body (16 USC §661-667e).
Migratory birds, including raptors, and active nests are protected under the MBTA. The MBTA prohibits
activities that result in taking, killing, or possessing migratory birds and their eggs. Possession of any nest
and destruction (without possession) of active nests that result in the loss of eggs or young is also
prohibited (16 USC §703-712). EO 13186 directs federal agencies to take certain actions to implement
the MBTA (86 Federal Register 3853, January 10, 2001).
The Bald and Golden Eagle Protection Act (16 USC § 668-668d) includes several prohibitions not found in
the MBTA, such as molestation or disturbance. In 1962, the act was amended to include the golden
eagle. In 2007, the term “disturb” was defined to mean “to agitate or bother a bald or golden eagle to a
degree that causes injury to an eagle, a decrease in productivity, or nest abandonment, by substantially
interfering with normal breeding, feeding, or sheltering behavior” (72 Federal Register 31332, June 6,
2007).
As directed by South Dakota Legislature (SDL) (Codified Law Chapter 34A-8), the South Dakota Game,
Fish, and Parks Commission (SDGFP) issues regulations and develops management programs
implemented by the SDGFP and the U.S. Department of Agriculture for wildlife species not federally
listed as threatened or endangered. This includes performing “those acts necessary for the conservation,
management, protection, restoration, and propagation of endangered, threatened, and nongame
species of wildlife” (SDL 2020).
Threatened and Endangered Species and State Special Status Species
Affected Environment
The Service lists several federally threatened and endangered species with potential habitat in Brown
County, or potentially affected by projects in Brown County (Table 1). State special status species
include species that are not protected under the ESA but are listed by SDGFP as threatened,
endangered, or of concern in South Dakota. State species considered imperiled are also included in
Table 1 (South Dakota Natural Heritage Program (SDNHP) 2020a).
Table 1. Federally threatened, endangered, and candidate species and state special status species
potentially found in the project area or potentially affected by the project.
Suitable Habitat
Present in Project area
Common Name Scientific Name Status* Habitat
or Potential to be
Affected by Project?
Mammals
Northern long-eared bat Myotis FT Caves and mines in winter; None; no suitable
septentrionalis woodlands with snags, rocky habitat in the project
outcrops, and large trees in area.
summer
12Houghton Dam Removal Project Environmental Assessment
Suitable Habitat
Present in Project area
Common Name Scientific Name Status* Habitat
or Potential to be
Affected by Project?
Northern river otter Lontra canadensis ST Rivers, streams, and lakes Low; may forage along
the James River near
the project area.
Unlikely to be affected
by the project.
Birds
Little blue heron Egretta caerulea SI Wetlands, marshes, and ponds Low; no suitable habitat
with nearby tree and shrub for breeding in the
cover project area.
Documented nests in
other areas of the
Refuge. Unlikely to be
affected by the project.
Red knot Calidris canutus rufa FT Tidal flats and sandy beaches Low; occasional
migrant. Unlikely to be
affected by the project.
Snowy egret Egretta thula SI Wetlands, marshes, and ponds Low; no suitable habitat
with nearby tree and shrub for breeding in the
cover project area.
Documented nests in
other areas of the
Refuge. Unlikely to be
affected by the project.
White-faced ibis Plegadis chichi SI Cattail marshes with nearby Low; no suitable habitat
hayfields and agricultural for breeding in the
areas for foraging project area.
Documented nests in
other areas of the
Refuge. Unlikely to be
affected by the project.
Whooping crane Grus americana FE, SE Mudflats around reservoirs Low; occasional migrant
and in agricultural areas in South Dakota.
Unlikely to be affected
by the project.
Fish
Topeka shiner Neotropis topeka FE Pools and slow-moving water No habitat; unlikely to
in headwater streams be affected by the
project.
Insects
Dakota skipper Hesperia dacotae FT Tall and mixed-grass prairie No habitat; unlikely to
dominated by native plants be affected by the
project.
*FT – Federally threatened, FE – Federally endangered, ST – State threatened, SE – State endangered, SI – State Imperiled
Sources: Service 2020; Service 2005; SDGFP 2021; SDNHP 2020a.
Northern Long-eared Bat (Myotis septentrionalis)
The northern long-eared bat is federally listed as threatened with the 4D rule. The northern long-eared
bat is a small bat, measuring an average of 3.4 inches in total length, with light brown fur and wing
membranes. Compared to other Myotis species, these bats have long ears with a relatively long tragus.
This species is known to hibernate in mines and caves with near constant temperatures and humidity.
During the summer months, the northern long-eared bat roosts in trees and snags with cracks and
crevices, and under tree bark. Its range is throughout the eastern and north-central United States
13Houghton Dam Removal Project Environmental Assessment
through southern Canada. In South Dakota, this species is mostly limited to riparian forests along the
Missouri River. The northern long-eared bat is one of the bats most affected by white-nose syndrome
with its numbers declining by 99 percent in northeastern caves and mines where it hibernates. There is
currently no evidence of northern long-eared bat populations recovering compared to other bat species.
Additional threats to this species include impacts on hibernation sites and loss or degradation of
summer habitat. Future environmental trends likely to affect this species include continued population
declines from white-nose syndrome. No future actions potentially affecting this species at the Refuge
are known.
Northern River Otter (Lontra canadensis)
The northern river otter is considered state threatened and is imperiled (S2) in South Dakota. The
northern river otter is a large mustelid that weighs between 11 and 30 pounds with short legs, a
muscular neck, and an elongated body. This species is found in streams, lakes, ponds, swamps, marshes,
and beaver flowages. When inactive, this species occupies hollow logs; spaces under roots, logs, or
overhangs; abandoned beaver lodges; dense thickets near water; or burrows of other animals. These
sites are also used for rearing young. Their range is throughout most of North America north of Mexico,
except the extreme southwestern United States. Tracks and individual otters were observed in the
Refuge in 2007. Loss of or degradation of habitat and water pollution are the main threats to this
species. As described for other threatened, endangered, or imperiled species, habitat change due to
climate change is a future trend that could affect this species. Future actions potentially affecting this
species include active management to benefit wetlands and other habitats at the Refuge as described in
the Vegetation and Wetlands sections.
Little Blue Heron (Egretta caerulea)
The little blue heron is considered critically imperiled (S1) in South Dakota. The little blue heron is a
small, dark heron with blue and purple plumage. Juvenile herons are white and transition to blue adult
plumage at the end of their first year. Little blue herons nest in shrubs or trees in standing water or on
reedbeds, foraging in nearby shallow marshes and pond edges. This species is found in the southeastern
United States, east and west coasts of Mexico, and the Caribbean. It is a rare but regular breeder in the
prairie potholes of the Dakotas, western Iowa, and western Minnesota (SDGFP 2012). Habitat change
due to climate change is a reasonably foreseeable future trend that could affect this species. This
species was last observed nesting in the Refuge in 1982 and has sporadically nested elsewhere east of
the Missouri River. This species is unlikely to be present in the project area due to lack of habitat. Future
actions potentially affecting this species include active management to benefit wetlands and other
habitats at the Refuge as described in the Vegetation and Wetlands sections.
Red Knot (Calidris canutus rufa)
The red knot is federally listed as threatened. Red knots are plump sandpipers with terracotta-orange
underparts and intricate gold, buff, rufous, and black upperparts during the breeding season.
Nonbreeding birds are gray with gray barring on the flanks. This species nests in the high Arctic and uses
undisturbed sandy beaches and tidal flats during the winter season. Its distribution is circumpolar and it
migrates from the southern hemisphere. In South Dakota, the red knot is a rare visitor and occasionally
uses lakes and wetlands as migration stopover sites. Threats to the red knot include declining
14Houghton Dam Removal Project Environmental Assessment
populations of horseshoe crabs in the Delaware Bay area, which provides an important food source for
this species, and hunting in their southern hemisphere habitat. Continued decline in populations of this
species is a reasonably foreseeable trend.
Snowy Egret (Egretta thula)
The snowy egret is considered imperiled (S2) in South Dakota. The snowy egret is a medium sized heron
with a black bill, black legs, yellow feet, and white plumage. During the breeding season, it has long,
recurved plumes on its back. This species nests in large marshes, flooded trees, or in trees and bushes
on islands, foraging in the shallow waters of wetlands. Its range is along the East and Gulf Coasts, the
lower Mississippi Valley, and the Great Basin. This species also breeds in scattered locations elsewhere
in the western United States and the Great Plains, including the eastern Dakotas (SDGFP 2012). Habitat
change due to climate change is a future trend that could affect this species. This species was first
observed nesting in the Refuge in 1977 and continues to nest in the northeastern part of the state, but is
unlikely to occur in the project area due to lack of suitable habitat. Future actions potentially affecting
this species include active management to benefit wetlands and other habitats at the Refuge as
described in the Vegetation and Wetlands sections.
White-Faced Ibis (Plegadis chichi)
The white-faced ibis is considered imperiled (S2) in South Dakota. The white-faced ibis is a long-legged
wading bird with a slender, decurved bill. It has red lores, a white border around the eyes, pink legs, and
purple, green, and bronze plumage. The white-faced ibis nests in large cattail marshes and forages in
flooded pastures and haylands, crop fields, damp meadows, and shallow marshes. It breeds in scattered
locations throughout the western United States and Great Plains, along the Gulf Coast, southern
California, and south into Mexico and South America. Their range in North America has expanded in
recent decades (SDGFP 2012). Habitat change due to climate change is a future trend that could affect
this species. This species is generally observed east of the Missouri River in South Dakota and has been
observed nesting in the Refuge in 2007 and 2010, but is unlikely to occur in the project area due to lack
of suitable habitat. Future actions potentially affecting this species include active management to
benefit wetlands and other habitats at the Refuge as described in the Vegetation and Wetlands sections.
Whooping Crane (Grus americana)
The whooping crane is federally listed and state listed as endangered. The whooping crane is tall bird
with bright white plumage and accents of red on the head. The legs, bill, and wingtips are black. This
species migrates between Port Aransas, Texas, and Wood Buffalo National Park, Canada. The whooping
crane has been seen at the Refuge from mid-October to mid-November. During migration, whooping
cranes use a variety of habitats; however, wetland mosaics appear to be the most suitable. Whooping
cranes primarily use shallow, seasonally and semipermanently flooded palustrine wetlands, and various
cropland and emergent wetlands, for feeding and roosting. The Refuge is outside of the designated final
critical habitat for this species. The main threat to whooping cranes in the wild is the potential of a
hurricane or contaminant spill destroying their wintering habitat on the Texas coast. Collisions with
power lines and fences are known hazards to wild whooping cranes. Habitat change due to climate
change, as described in the Vegetation section, is a future trend that could affect this species. Future
15Houghton Dam Removal Project Environmental Assessment
actions potentially affecting this species include active management to benefit wetlands and other
habitats at the Refuge as described in the Vegetation and Wetlands sections.
Topeka Shiner (Neotropis topeka)
The Topeka shiner is federally listed as endangered. The Topeka shiner is a small, silver minnow with a
black stripe running along the side of its body. This species typically inhabits quiet, open, permanent
pools of small, clear, high-quality headwaters and creeks that drain upland prairie areas, including tiny
spring-fed pools in headwater streams and larger streams. The Topeka shiner is found in small pockets
in Iowa, Kansas, Minnesota, Missouri, Nebraska, and South Dakota. In South Dakota, this species is
found along the Elm River. The Refuge is outside the designated final critical habitat for this species.
Threats to the species include habitat destruction, sedimentation, and changes in water quality. No
future actions at the Refuge are expected to affect this species because it is unlikely to be present.
Dakota Skipper (Hesperia dacotae)
The Dakota skipper is federally listed as threatened. The Dakota skipper is a small butterfly with a
wingspan of approximately 1 inch. Males have tawny orange forewings with a prominent mark and
dusty yellow back wings. The females are darker orange with white spots on the forewing margin. This
species is dependent on tallgrass and mixed-grass prairie habitat. As of 2002, this species was limited to
150 sites in Canada and the northern midwestern states. The Refuge is outside the designated final
critical habitat for this species. Dakota skipper populations declined historically because of widespread
conversion of native prairie to farms, ranches, and other land uses. Habitat change due to climate
change is a future trend that could affect this species. No future actions at the Refuge are expected to
affect this species because it is unlikely to be present due to lack of habitat.
Environmental Consequences
Alternative A
Alternative A would not affect the northern long-eared bat, red knot, whooping crane, Topeka shiner, or
Dakota skipper (federally listed threatened or endangered species) because of lack of suitable habitat.
The northern long-eared bat requires trees, woodlands and snags for roosting. No trees or snags are
located in the project area. Therefore, Alternative A would not affect the northern long-eared bat.
The red knot is an infrequent migrant in South Dakota, and no breeding of this species has ever been
documented in the state. While the red knot could briefly use the Refuge during migration, it is unlikely
that the red knot would roost or forage in the project area due to lack of cover and tall vegetation.
Therefore, Alternative A would not affect the red knot.
The whooping crane is dependent on wetlands for roosting and feeding during migration. Alternative A
would impact 0.04 acre (1,740 square feet) of wetland vegetation along an upland-wetland transition
zone habitat area on either side of the dam. However, the Refuge has more than 11,000 acres of higher
quality wetland habitat that would not be impacted by the project. Additionally, the whooping crane is
only an occasional migrant through this portion of South Dakota. Therefore, Alternative A would not
affect the whooping crane.
16Houghton Dam Removal Project Environmental Assessment
The Topeka shiner is dependent on small, headwater streams of the James River and avoids larger water
bodies. The project area is located along the mainstem of the James River and does not contain habitat
for this species. Therefore, Alternative A would not affect the Topeka shiner.
The Dakota skipper requires tall and mixed grass prairie. The project area does not contain expanses of
tall or mixed grass prairie that this species requires. Therefore, Alternative A would not affect the
Dakota skipper.
The remaining state-listed species (northern river otter, little blue heron, snowy egret, and white-faced
ibis) have the potential to occur within wetlands and open water adjacent to the proposed project area.
The majority of project activities would occur over a small area compared to the abundance of higher
quality habitat in other areas of the Refuge, and the majority of the effects on wetlands and open water,
which these species favor, would mostly be temporary; therefore, it is unlikely that Alternative A would
affect these species, or even temporarily displace individuals.
Overall, temporary or permanent impacts from Alternative A would not affect habitat for any federally
listed species or state special status species.
Alternative B
Alternative B would not result in any new impacts on any federally listed threatened or endangered
species or special status species. Existing conditions within and in the vicinity of the project area would
not change under Alternative B.
Additional Sensitive Bird Species Known to Occur at the Refuge
Affected Environment
Table 2 contains a list of grassland bird species that are considered sensitive by Partners in Flight (PIF),
the Service, The Nature Conservancy (TNC), or the SDNHP and have been documented at the Refuge.
Table 2. Additional sensitive bird species known to occur at the Refuge.
Suitable Habitat
Common Name Scientific Name Status Habitat Present or Potential to
be Affected?
American bittern Botaurus PIF, Wetlands, marshes, and Habitat present at the
lentiginosus Service ponds with nearby tree and Refuge. Unlikely to be
shrub cover affected by the project.
Chestnut-collared Calcarius ornatus PIF, Tidal flats and sandy beaches Low; occasional
longspur Service, migrant. Unlikely to be
TNC affected by the project.
Dickcissel Spiza americana Service, Wetlands, marshes, and Low; no suitable habitat
Audubon ponds with nearby tree and for breeding. Could
shrub cover occasionally forage at
the Refuge.
Grasshopper sparrow Ammodramus PIF, Cattail marshes with nearby Habitat present at the
savannarum Service hayfields and agricultural Refuge. Unlikely to be
areas for foraging affected by the project.
LeConte’s sparrow Ammodramus PIF, Mudflats around reservoirs Low; occasional migrant
leconteii Service, and in agricultural areas in South Dakota.
SDNHP Unlikely to be affected
by the project.
17Houghton Dam Removal Project Environmental Assessment
Suitable Habitat
Common Name Scientific Name Status Habitat Present or Potential to
be Affected?
Loggerhead shrike Lanius ludovicianusi Service Pools and slow-moving water No habitat. Unlikely to
in headwater streams be affected by the
project.
Marbled godwit Limosa fedoa PIF, Tall and mixed-grass prairie No habitat. Unlikely to
Service, dominated by native plants be affected by the
Audubon project.
Nelson’s sharp-tailed Ammodramus PIF, Tall, dense grass in Habitat present at the
sparrow nelsoni Service, freshwater marshes and Refuge. Unlikely to be
Audubon, surrounding wet meadow affected by the project.
SDNHP zones
Northern harrier Circus cyaneus PIF, Treeless habitats such as Habitat present at the
Service wetlands, agricultural areas, Refuge. Unlikely to be
wet meadows, pastures, affected by the project.
fallow fields, and native
prairies
Sharp-tailed grouse Tymphanuchus PIF Open grasslands mixed with No habitat. Unlikely to
phasianellus shrubs, forest edges and be affected by the
clearings, open burns and project.
clear cuts in coniferous
forests, and wooded draws;
requires large amounts of
grasslands
Short-eared owl Asio flammeus PIF, Marshes and grasslands that Habitat present at the
Service, provide dense cover for Refuge. Unlikely to be
Audubon nesting affected by the project.
Swainson’s hawk Buteo swainsoni PIF, Open prairie and agricultural No habitat. Unlikely to
Service, areas that have some trees be affected by the
Audubon, for nesting project.
SDNHP
Upland sandpiper Bartramia PIF, Large areas of dry grasslands No habitat. Unlikely to
longicauda Service that offer a mix of vegetation be affected by the
heights project.
Willet Tringa semipalmata PIF, Nests in grasslands near Habitat present at the
Service shallow wetlands Refuge. Unlikely to be
affected by the project.
Wilson’s palarope Phalaropus tricolor PIF, Shallow ponds and marshes, Habitat present at the
Service, wet meadows, and wet Refuge. Unlikely to be
Audubon ditches affected by the project.
Sources: Service 2005; SDGFP 2012, 2021; SDNHP 2020b.
Habitat change due to climate change and resulting changes in fire regime or habitat degradation due to
the spread of invasive plants are future trends that could affect these species. For species that have
potential habitat at the Refuge, beneficial effects would result from reasonably foreseeable future
actions at the Refuge such as the Refuge’s active management of upland and wetland habitat to benefit
waterfowl and other migratory birds.
Environmental Consequences
Alternative A
The American bittern, dickcissel, grasshopper sparrow, LeConte’s sparrow, loggerhead shrike, Nelson’s
sharp-tailed sparrow, short-eared owl, willet, and Wilson’s phalarope all depend on wetlands for
roosting, nesting, and feeding during migration. Alternative A would impact about 0.02 acre (871 square
18Houghton Dam Removal Project Environmental Assessment
feet) of wetland vegetation along an upland-wetland transition zone habitat area on either side of the
dam. Because the majority of project activities would be limited to a small area, the effects on terrestrial
species including chestnut-collared longspur, marbled godwit, northern harrier, sharp-tailed grouse,
Swainson’s hawk, and upland sandpiper would be minimal, and most effects would likely be temporary.
Therefore, it is unlikely that Alternative A would affect these species, or even temporarily displace
individuals.
Alternative B
Alternative B would not result in any new impacts on any sensitive bird species. Existing conditions
within and in the vicinity of the project area would not change under Alternative B.
Other Migratory Birds and Raptors
Affected Environment
Songbirds, raptors, shorebirds, and waterfowl breed, overwinter, or migrate through the Refuge. The
Refuge has been designated as a Globally Important Bird area and a Wetland of International
Importance, and historically supported the world’s largest population of Franklin’s gulls (Leucophaeus
pipixcan). This area provides sanctuary and roosting areas for migratory birds. The project area consists
mostly of open water, although fringes of cattail wetlands border the edge of the dam. Common
waterfowl and marsh and water birds observed in the Refuge include blue-winged and green-winged
teals, wood duck, American white pelican, giant Canada goose, snow goose, double crested cormorant,
great blue heron, black-crowned night heron, pied-billed grebe, western grebe, eared grebe, American
avocet, cattle egret, and Forster’s tern. Other common migratory birds include red-winged blackbird,
yellow-headed blackbird, American robin, horned lark, yellow warbler, and bobolink. In addition to
Swainson’s hawk and northern harrier mentioned above in Table 2, red-tailed hawk and bald eagle also
occur near or within the Refuge. Bald eagle nesting has increased in recent years near and within the
Refuge. As described above for sensitive bird species, habitat change due to climate change and
resulting changes in fire regime or habitat degradation due to the spread of invasive plants are future
trends that could affect these species. Reasonably foreseeable future actions that could affect other
migratory birds and raptors include the Refuge’s active management of upland and wetland habitat to
benefit waterfowl and other migratory birds.
Environmental Consequences
The primary nesting season for migratory birds in eastern South Dakota is from April to early August
(although varies by species). Some birds such as red-tailed hawk and bald eagle nest earlier (SDGFP
2021).
Alternative A
Alternative A may temporarily displace some waterfowl that are passing through the area and could
disrupt some individuals that are roosting in adjacent cattail stands. The project would impact about
0.02 acre of wetland habitat during construction. Temporary effects from access and staging may
temporarily displace individuals; however, Alternative A would not adversely affect the overall
population of nesting birds in the project area because of the abundance of similar surrounding habitat
and nearby undisturbed areas.
19Houghton Dam Removal Project Environmental Assessment
Alternative B
Alternative B would have no effect on migratory birds and raptors because there would be no removal
of existing vegetation, and areas of open water would not be disturbed.
Large Game
Affected Environment
The project area is located within the overall range for pronghorn, mule deer, white-tailed deer, and
black bear (Armstrong et al. 2011). Pronghorn, mule deer, and black bear are not as common in this
portion of northeastern South Dakota as white-tailed deer. Large game on the Refuge, particularly
white-tailed deer, are economically important species in South Dakota. The Refuge contains a large
population of white-tailed deer that are managed and hunted. Hunting and habitat management at the
Refuge are future actions that affect large game species. These activities are be carried out in
accordance with the Refuge’s Comprehensive Conservation Plan (Service 2005) and would not adversely
affect these species at the population level.
Environmental Consequences
Alternative A
Alternative A would not adversely affect any large game on the Refuge. The project area consists of
mostly open water with a narrow strip of earthen dam. The project may have temporary effects on large
game from construction equipment access and staging. Individual large game animals may avoid areas
where construction equipment is mobile or being staged. Alternative A would have no permanent
adverse effects on large game species.
Alternative B
Alternative B would have no effect on large game because there would be no removal of existing
vegetation, and areas of open water would not be disturbed.
Vegetation
Affected Environment
Vegetation across the Refuge varies. Wetlands (marsh and open water) encompass 11,450 acres of the
Refuge. The remaining vegetation communities include 9,300 acres of grasslands, about 500 acres of
croplands, and about 400 acres of shelterbelts.
Vegetation management on the Refuge is focused on enhancing native vegetation to provide diversified
habitat for wildlife and to reduce nonnative vegetation. The Refuge’s vegetation management direction
includes:
• Reducing cropland acreage;
• Discontinuing planting of additional shelterbelts and letting existing shelterbelts die off;
• Removing invasive species, including stands of Russian olive (Elaegnus angustifolia) trees;
• Applying native seed in areas where invasive species or cropland has been removed; and
• Performing prescribed burning when warranted.
20Houghton Dam Removal Project Environmental Assessment
The Refuge plans to attempt to replace some large stands of smooth brome (Bromus inermis) in upland
areas with tall, dense native vegetation that provides adequate cover for nesting birds.
The Refuge contains three primary habitat types: wetlands, grasslands (including croplands), and
woodlands (including shelterbelts).
Wetland communities are described in the Wetlands section below but are largely dominated by cattail
(Typha sp.), common reed (Phragmites australis), and some grasses, rushes, and sedges. Plains
cottonwood (Populus deltoides) and sandbar willow (Salix exigua) trees often occur around the
periphery of wetlands.
Grassland communities consist largely of exotic species such as smooth brome and alfalfa (Medicago
sativa). The Refuge is restoring some croplands that are out of production to native grasslands. A
combination of native mid- and tallgrass species including little bluestem (Schizachyrium scoparium), big
bluestem (Andropogon gerardi), Indiangrass (Sorghastrum nutans), green needlegrass (Nassella
viridula), sideoats grama (Bouteloua curtipendula), switchgrass (Panicum virgatum), and western
wheatgrass (Pascopyrum smithii) are being planted in restored areas.
Woodlands occur along portions of the James River mainly south of the Refuge. Common trees and
shrubs include plains cottonwood, American elm (Ulmus americana), green ash (Fraxinus
pennsylvanica), boxelder (Acer negundo), and various willows (Salix sp.). Shelterbelt communities
consist of woodlands that were planted in 1937 and 1938 to provide wildlife habitat and protect the
area from extreme weather and erosion. American elm, Chinese elm (Ulmus parvifolia), and green ash
were the most common trees planted in the shelterbelts. Most shelterbelts are currently not managed
and are deteriorating due to previous Dutch elm disease outbreaks.
Currently, approximately 500 acres of cropland are managed on the Refuge through various
cooperators. Crops are rotated between corn, soybeans, and spring wheat. The Refuge cooperators
manage the crops, and the Refuge is entitled to 25 percent of the shared crops, which are often left
standing to produce food for white-tailed deer and waterfowl.
Future trends that could affect vegetation at the Refuge include encroachment by invasive plant species
and climate change. The South Dakota Department of Agriculture (SDDOA) monitors weed populations
throughout the state (SDDOA 2021). Of the six noxious weeds identified by the SDDOA, two are
common on the Refuge – Canada thistle (Cirsium arvense) and leafy spurge (Euphorbia esula). Canada
thistle is the most prominent invasive species on the Refuge, which can dominate the wetland/upland
transition zone. Other invasive plants include Russian olive (Eleagnus angustifolia) and wormwood
(Artimesia annua).
Climate change, whether it results from anthropogenic or natural sources, is expected to affect a variety
of natural processes and associated resources. However, the complexity of ecological systems means
that there is a tremendous amount of uncertainty about the impact climate change will have. In
particular, the localized effects of climate change are still a matter of much debate. That said, the
combination of changes in precipitation patterns or increased frequency and severity of drought and
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