MANAGING MINNESOTA’S SHALLOW LAKES FOR

WATERFOWL AND WILDLIFE

Shallow Lakes Program Plan

Minnesota Department of Natural Resources

Division of Fish and Wildlife

Wildlife Management Section

December 2010
ii
TABLE OF CONTENTS

LIST OF FIGURES AND TABLES ..............................................................2

EXECUTIVE SUMMARY................................................................................................. 3

INTRODUCTION..........................................................................................4

STATEWIDE SHALLOW LAKE MANAGEMENT GOAL: MANAGEMENT 

AND PROTECTION OF 1800 SHALLOW LAKES ACROSS THE STATE 

FOR THE BENEFIT OF WATERFOWL AND WILDLIFE............................6

Objective 1: Fully assess habitat of Minnesota’s shallow lakes and document resource 

condition, determine management potential and evaluate results of 

management activities on the subset of shallow lakes that are actively 

managed.................................................................................................... 7

Objective 2: Maximize management of shallow lakes for waterfowl and wildlife habitat 

that are designated as wildlife management lakes or are within public 

lands. ......................................................................................................... 9

Objective 3: Maximize management of shallow lakes for waterfowl and wildlife that are 

adjacent to public lands managed specifically for wildlife or public lands 

with wildlife habitat value. ........................................................................ 12

Objective 4: Increase waterfowl and wildlife habitat in shallow lakes with public access 

that do not have tracts of shoreline specifically managed for wildlife....... 17

Objective 5: Increase awareness and protection of lakes containing measurable stands 

of wild rice................................................................................................ 21

BACKGROUND.........................................................................................23

Basic Shallow Lake Ecology and Management............................................................. 23

Shallow Lakes in Minnesota.......................................................................................... 25

SHALLOW LAKE MANAGEMENT FOR WILDLIFE.................................30

THE CHALLENGES...................................................................................................... 32

OPPORTUNITIES AND MANAGEMENT APPROACHES............................................ 39

Direct Protection.............................................................................39

Habitat and Water Quality Improvement Tools ............................40

Regulatory Tools for Protection of Shallow Lakes and Wildlife 

Resources .......................................................................................43

LITERATURE CITED.................................................................................46

APPENDIX A: DISTRIBUTION MAPS OF SHALLOW LAKES 

TARGETED FOR MANAGEMENT............................................................50
2

List of Figures and Tables

Figure 1. Pre and post-management aquatic plant survey data from 

recently managed shallow lakes. Pre-management data was 

collected at least one year prior to management action, postmanagement data was collected 1-3 years after a specific 

management action.

9

Table 1. Shallow lakes by Ecoregion, Program Plan objectives 

and public land category

20

Figure 2. Shallow lake distribution in Minnesota by Ecoregion 23

Figure 3. Summary of shallow lake conditions in Minnesota 24

Table 2. General shallow lake information. There is overlap in lakes in 

each category, for example, wild rice lakes may also be counted 

in lakes associated with public lands, or a Designated Wildlife 

Lake could also have a MWFRA.

25

Figure 4. Wild rice distribution in Minnesota 27

Figure 5. Projected population change in Minnesota by county, data from 

State Demographer’s Office

28

Figure 6. Lakes designated as Wildlife Management Lakes under M.S. 

97A.101

29

Figure 7. Distribution of shallow lakes with recreational fisheries or 

aquaculture use

30

Table 3. Impacts to shallow lakes and potential management tools 31

Figure 8. Precipitation data for Otter Tail County, MN from 1973-2009. 

Annual averages by decade based on all available data in Otter 

Tail County from Minnesota State Climatology records

32

Figure 9. Average date of lake ice out from historical data on several lakes 

across the state

37
3

EXECUTIVE SUMMARY

The following goals for management and protection of shallow lakes have 

been identified in order to: meet the objectives in the Minnesota Department 

of Natural Resources’ (DNR) Long Range Duck Recovery Plan (Duck Plan) 

and Division of Fish and Wildlife Strategic plan, and provide focus to shallow 

lake management efforts undertaken by the DNR Section of Wildlife 

Management.

The goal in the Duck Plan is to protect and manage at least 1,800 shallow 

lakes in Minnesota for their ecological, recreational, and economic importance 

to the citizens of the state with particular emphasis on wildlife and wildlifebased recreation. A shallow lake is defined as a lake that is at least 50 acres 

in size and no more than 15 feet deep. The objectives of this plan provide 

focus and criteria for identifying on which lakes to focus management efforts 

to insure the DNR is maximizing waterfowl and wildlife habitat on shallow 

lakes associated with public wildlife lands.

There are approximately 4,000 shallow lakes in the state; 1,000 of these 

lakes are currently managed for sport fisheries or used for aquaculture. 

Management of all of these lakes is not needed, nor possible, to achieve the 

goals of the Duck Plan or the Shallow Lake Program Plan (Program Plan). 

The following objectives are aimed at managing those basins with high 

wildlife management potential and maximum wildlife and public benefit. 

Progress towards the goals of the Duck Plan and the Program Plan will be 

measured by the following long-term objectives: 

1) Assess habitat conditions of Minnesota’s shallow lakes

2) Maximize management of all 200 shallow lakes within state Wildlife 

Management Areas (WMAs), federal Waterfowl Production Areas (WPAs), 

and National Wildlife Refuges (NWRs) and all state Designated Wildlife 

Management Lakes (DWLs) for high quality waterfowl habitat

3) Maximize management of the ~1,553 shallow lakes with a portion of their 

shorelines under state, federal or county ownership for high quality 

waterfowl habitat, including designation of an additional 30 lakes

4) Increase wildlife management of the 201 shallow lakes with public access, 

but no other large tracts of public land, especially those lakes that already 

are designated as Migratory Waterfowl Feeding and Resting Areas 

(MWFRAs) or have wildlife habitat

5) Increase awareness of the historic, cultural and natural resource benefits

of wild rice and protect lakes containing natural stands of wild rice
4

INTRODUCTION

Minnesota has long recognized the role of shallow lakes for providing critical waterfowl 

and wildlife habitat. The definition of a shallow lake used in this plan is a lake that is 50 

acres or greater in size and has a maximum depth of 15 feet or less. Several key 

shallow lakes have been actively managed for wildlife benefits for decades. Despite 

management of select shallow lakes, the overall condition of the resource has declined. 

Recently, the DNR and others have given renewed attention to the condition of the 

state’s shallow lakes partly due to the decline in quality of waterfowl hunting and 

growing concern over poor water quality in many of these lakes.

The DNR released a new “Long Range Duck Recovery Plan” (Duck Plan) on April 21, 

2006. This plan identified a strategic 50-year vision to restore, protect and manage a 

Minnesota landscape capable of supporting an average spring breeding population of 

one million ducks and restoring the historically abundant spring and fall migration of 

waterfowl. This landscape would also provide sufficient opportunities to support 

140,000 waterfowl hunters and 600,000 waterfowl watchers.

Minnesota’s shallow lakes are key components to this vision of a productive landscape

for waterfowl. No other state has the diversity or quantity of shallow lake resources that 

Minnesota can provide. From the large prairie lakes to wild rice bays bordered by 

forest, the state has a unique resource that has been taken for granted and abused. 

These lakes provide habitat for many species of wildlife including waterfowl, other water 

birds, furbearers, amphibians, reptiles and fish. The Duck Plan suggests that at least 

1,800 shallow lakes, almost half of the total resource, will have to be protected and 

managed if the state is going to achieve the targets set for recovery of duck populations. 

Shallow lakes are important migration habitats as well as breeding habitats for overwater nesting species of waterfowl. Favored habitats are those that have thick stands 

of emergent vegetation including cattail, bulrush or sedge. Canvasbacks, redheads, 

mallards and ruddy ducks are all species that will nest over-water in emergent 

vegetation (Baldassarre and Bolen, 2006). This valuable breeding habitat has 

decreased with higher water levels in lakes and wetlands over the last two decades. 

Diving ducks (canvasbacks, redheads, lesser scaup and ring-necked ducks) rely on 

lakes especially for both spring and fall migration habitat (Korschgen 1989). In the 

spring, it is important that these lakes provide abundant invertebrates to support female

ducks that are preparing to breed and nest. For example, lipid and mineral reserves are 

important determinants of nest initiation and clutch size in lesser scaup (Anteau and 

Afton 2004). There is evidence that the quality of spring migration habitat in Minnesota 

has declined, particularly in the abundance of important invertebrates such as 

amphipods. Anteau and Afton (2006) attribute the decrease in lipid reserves to a 

corresponding decrease in the amount of amphipods in the diets of scaup during spring 

migration. Both invertebrates and plants are important nutrient sources to diving ducks 

in the fall. Ducks need to feed on these food sources relatively undisturbed to gain 
5

weight for the remaining migration (Korschgen 1989). Thus it is important that shallow 

lakes provide both invertebrates and aquatic plants in order to meet migrational habitat 

needs of waterfowl.

Shallow lakes are important habitats for many species of wildlife beyond waterfowl. 

Many have large numbers of colonial nesting water birds (key example lakes are Thief, 

Marsh, and Christina). These lakes also provide important habitat to many 

environmentally sensitive species and species listed as having the “greatest 

conservation need” by the DNR in Tomorrow’s Habitat for the Wild and Rare (THWR). 

Over 20 species listed as a species of greatest conservation need (SGCN) utilize 

shallow lake habitats (DNR 2006). 

While the need to manage and protect shallow lakes currently exists, there are 

potentially dramatic shifts on the horizon that will further impact shallow lakes and their 

watersheds. These possible impacts include: changes in population demographics, 

land use changes, increased water demands, climate change, and invasive species. 

Because of these and a myriad of other issues, waterfowl and wetland managers are 

beginning to recognize that land protection through acquisition or easements is not 

enough to provide quality habitat or maintain water quality. The implications of these 

multiple impacts necessitate the need for active management of aquatic habitats and 

watersheds for wildlife and waterfowl (Baldassarre and Bolen, 2006). The benefits of 

active management to waterfowl migration habitat have long been recognized 

(Korschgen 1989). Active management may include drawdowns, herbicide treatments, 

rotenone treatments or other manipulations of fish communities, and managing run-off 

through wetland and grassland restoration. Likewise, in order for the state to have 

quality waterfowl habitat, active management and further protection of shallow lakes are 

necessary along with the strategies outlined in the State’s Duck Plan. 

This plan is a broad plan to guide wildlife management activities on shallow lakes over 

the next 45 years (the same time frame as the Duck Plan) but also provides short-term 

implementation targets and evaluation of habitats and management. The primary 

purpose of this plan is to provide focus to wildlife and waterfowl management activities

on shallow lakes. However, a broader interest in the water quality of shallow lakes is 

also emerging as evidenced by the emphasis of shallow lake restoration in the recent 

Minnesota Statewide Conservation and Preservation Plan. Active management is also 

needed to achieve objectives beyond wildlife and waterfowl habitat, such as improving

and protecting basic water quality in these lakes. Active management could include 

actions such as drawdowns and watershed restoration to improve or protect habitat or 

water quality. Broader management strategies could be developed to address those 

water quality needs that may also provide some wildlife and waterfowl habitat benefits. 

Such plans would likely require greater resources and more partners than are currently 

available for wildlife and waterfowl management purposes.

In the future, many shallow lakes will likely be determined to be impaired for nutrients as 

defined by the Clean Water Act. Total Maximum Daily Load (TMDL) studies and plans 

will then be required for the impaired basins. Strategies to improve water quality 
6

through the TMDL process will likely focus on watershed restoration and management;

however, the internal nutrient loading in these lakes will also need to be addressed to 

achieve noticeable water quality improvements. While the specific goals of TMDL plans 

are not generally to improve wildlife and waterfowl habitat, improvements in water 

quality will benefit wildlife habitat on shallow lakes.

The potential to manage shallow lakes is broad; this program plan provides a framework 

to manage shallow lakes associated with public lands which are specifically managed 

for wildlife purposes. While these criteria provide an overall approach, it is not meant to 

prevent area staff from implementing approaches and strategies that make sense at the 

local level. It does establish that Designated Wildlife Lakes (DWLs) or shallow lakes 

within and adjacent to Wildlife Management Areas (WMAs), United States Fish and 

Wildlife Service (FWS) Waterfowl Production Areas (WPAs), State Forests, State Parks

and other public lands of high wildlife value should provide the cornerstones of 

waterfowl migration habitat in the state. Once the management needs of those lakes 

associated with public wildlife lands in a particular area have been adequately 

addressed, then management could be expanded to additional lakes.

STATEWIDE SHALLOW LAKE MANAGEMENT GOAL: Management and protection 

of 1,800 shallow lakes across the state for the benefit of wildlife and waterfowl.

This broad goal requires comprehensive strategies to improve wildlife and waterfowl 

habitat in shallow lakes across the state. An additional benefit of active management 

for high-quality habitat may also be improved water quality in these lakes. The following 

objectives have been identified in order to meet the above goal, to meet objectives 

related to shallow lakes in the state’s Duck Plan, to implement some suggestions from 

the Wild Rice Legislative Report, and finally to provide wildlife managers with tools and 

criteria to focus shallow lake management efforts and activities that will maximize 

waterfowl and wildlife habitat while also providing public benefit.

There are just over 4,000 “shallow lakes” in the state – lakes that are 50 acres or 

greater in size and have a maximum depth of 15 feet or less. Management of all of 

these lakes is not possible or needed to achieve the goals of the Duck Plan or the 

Shallow Lake Program Plan. Resources are always limited, and it is critical to prioritize 

where resources will be allocated. Management focused on shallow lakes associated 

with public land managed for wildlife purposes or managed in part for wildlife value 

should form the basis of waterfowl migration habitat in the state. In many cases active 

shallow lake management can enhance both breeding and migration habitats in these 

lakes. Shallow lakes within or adjacent to WMAs and WPAs, State Forests, State Parks

or county lands should be in good habitat condition, but often direct protection through 

fee title acquisition or conservation easements is not enough to insure quality habitat 

exists in these lakes. As the primary agency responsible for habitat management, it is 

critical that DNR staff are making every effort to provide quality habitat on shallow lakes 

where the DNR owns shoreline. These lakes should provide the foundation of 

waterfowl migration habitat throughout the state and set the example of the quality of

habitat that can be provided through protection and management.
7

The following objectives are aimed at managing those basins with high management 

potential and maximum wildlife benefit. Progress towards the goal of 1,800 managed 

shallow lakes will be measured by progress towards the following long-term objectives: 

1) Assess shallow lakes for management need and potential,

2) Maximize management of shallow lakes for waterfowl and wildlife habitat that 

are designated as wildlife management lakes or are within public lands, 

3) Maximize management of shallow lakes for waterfowl and wildlife that are 

adjacent to public lands with wildlife habitat, 

4) Increase waterfowl and wildlife habitat in shallow lakes with public access that 

do not have tracts of shoreline specifically managed for wildlife, 

5) Designate “Important Wild Rice Lakes” to further increase awareness of the 

historic, cultural and habitat importance of wild rice.

The department currently manages approximately 300 shallow lakes for wildlife 

resource benefits across the state. An additional 1,500 lakes must be added to meet 

the goals of the duck plan. A 45-year time frame with annual implementation targets is 

set to achieve this goal.

Objective 1: Fully assess habitat of Minnesota’s shallow lakes and document 

resource condition, determine management potential, and evaluate results of 

management activities on the subset of shallow lakes that are actively managed.

Justification:

In recent years with the addition of full-time staff and seasonal interns, the 

number of surveys on shallow lakes has increased. Yet, a large number of 

shallow lakes have not been surveyed within the last 10 years or have never 

been surveyed at all. Certainly additional management opportunities exist, and 

basins in good condition need to be identified so preservation and protection 

efforts can be prioritized. Completed surveys have helped determine conditions 

of shallow lakes at regional- and lake-level scales. However, due to the dynamic 

nature of these lakes over relatively short time periods, the constant threat of 

invasive species, and future consequences of climate change, continued surveys 

are necessary to provide up-to-date knowledge of the condition of the resource. 

These surveys also provide a measure of management success and provide 

information on management failures that may be used in future management 

decisions. Habitat and water quality information prior to and after management 

are necessary to develop adaptive management strategies. 

Primary Strategies:

Assess lakes using established lake survey protocols for shallow lake 

surveys (including water quality sampling)

Utilize remote sensing tools as technologies become more advanced

Employ invertebrate and fish sampling on a subset of basins
8

Assess/monitor potential stressors (e.g. watershed size, crop coverage, 

feedlots, ditches or tiles, impervious surface, near shore development) to 

determine management feasibility

Assess outlet condition where water level management may be 

appropriate

Target 1a: Conduct initial habitat assessments on all 1,954 shallow lakes 

associated with public land within 10 years.

Implementation:

Survey a minimum of 200 lakes per year

Coordinate with State Park staff to determine highest priority shallow lakes 

within/adjacent to State Parks that are in need of habitat surveys

Develop and evaluate additional assessment techniques through 

partnership with research groups and other entities

Maintain the Wildlife Lake Database to organize survey data and produce 

survey reports on demand 

Make habitat survey reports available on the DNR internet site

Maintain and update as needed the list of managed wild rice lakes

Target 1b: Conduct periodic surveys to evaluate habitat conditions on those 

lakes that are actively managed to support adaptive management strategies.

Implementation:

Survey lakes within two years after a management action

Maintain the Wildlife Lake Database to organize survey data and produce 

survey reports on demand 

Maintain and update as needed the list of managed wild rice lakes

Partner with the Wetland Wildlife Research Group and Universities on 

research that will lead to improvements in management abilities and 

opportunities on shallow lakes

Objective 1 Operational Plan:

Seven two-person, out-fitted field survey crews per summer 

Four additional specialists to oversee field crews 

Provide specific training to field crews for invasive species identification

One specialist serving as the Statewide Field Survey Coordinator

One specialist dedicated to maintain database and manage data

One specialist dedicated to enter survey data into database and produce 

survey reports

Partner with other agencies or provide data to other agencies that are also 

charged with assessing water quality in the state’s lakes

Continue to monitor habitat on Shallow Lake Case Study Lakes

Schedule coordination meetings with DNR Wetland Research as needed 

to explore new survey and assessment tools, techniques, and methods
9

Provide pre-management data to Wetland Wildlife Research for shallow 

lake research project

Schedule regular coordination meetings with DNR Regional Wildlife Staff

Objective 2: Maximize management of shallow lakes for waterfowl and wildlife 

habitat that are Designated Wildlife Lakes or are located completely within public 

lands.

Justification: Designated Wildlife Lakes, shallow lakes and wild rice lakes 

within Wildlife Management Areas, Waterfowl Production Areas, and National 

Wildlife Refuges (NWRs) should have high quality habitat. While some of these 

lakes are currently actively managed, additional opportunities for increased 

management and habitat improvement still exist across the state. Many of these 

lakes have dilapidated water control structures in need of replacement, and some 

designated lakes have never been actively managed.

The shallow lakes located completely within these areas of public ownership 

have protection from shoreline development and often have large areas of 

upland buffers; however this protection has not insured that these basins have 

high quality wildlife and waterfowl habitat. As with other shallow lakes, many of 

the lakes within these areas of public ownership are impacted by invasive 

species, excessive nutrient loading, and climate change. Monitoring data on 

some lakes that are actively and intensively managed shows dramatic 

improvements in habitat and water quality can be achieved (Figure 1).

Figure 1. Pre and post-management aquatic plant survey data from recently managed shallow 

lakes. Pre-management data was collected at least one year prior to management action; postmanagement data was collected 1-3 years after a specific management action.
10

The Shallow Lakes Program places a high priority on assessing habitat 

conditions on DWLs or basins completely within public land. Those lakes with 

outlets may have drawdown potential; those lakes without outlets could be 

potential rotenone treatment candidates. While the authority to manage basins 

within federal public wildlife lands lies with the FWS, the DNR can and does work 

cooperatively to provide technical assistance and survey information on these 

basins to encourage active management for high quality habitats. There are 

some basins where both agencies own shoreline and management is a 

cooperative effort.

Managing these lakes also is consistent with goals in the Duck Plan to manage 

habitat in complexes of grasslands, wetlands and shallow lakes. Most of the 

shallow lakes identified in this category already are a part of, or the start of, a 

complex of wetland, grassland, or other natural habitats.

Primary Strategies:

A part of achieving this objective includes a change to the current statutory 

language in 97A.101 to allow regulation of bait harvest (minnows as 

defined in 97A.015 Subd. 29) in Designated Wildlife Lakes. 

Rational: The Section of Wildlife spends great amounts of resources on 

management of individual lakes, especially Designated Wildlife Lakes (DWLs). 

Much of this management is aimed at managing or minimizing fish populations in 

these lakes; however Wildlife has no authority to regulate the use of these basins 

for bait trapping activities. While it may not be necessary to restrict bait trapping 

on all DWLs, it would be beneficial to have the option as another management 

tool. Such regulation could be used to limit disturbance during the waterfowl 

nesting season, protect high quality brood habitat, or to protect against exotic 

species introduction. Such protections exist for basins within WMAs, so it is 

reasonable and logical to consider extending the same protections to DWLs. 

Also, regulations restricting bait harvest already apply to waters infested with 

certain invasive species. 

Potential regulation options include limiting the time of year bait could be 

harvested, completely prohibiting bait harvest, or allowing bait harvest by special 

permit only.

 Additional Strategies:

In-Lake Management

o Water level management including installation of permanent water 

control structures or use of temporary pumps or siphons

o Rotenone treatments to manage fish populations (best conducted on 

isolated lakes or groups of lakes)

o Maintenance of water levels through beaver dam removal and outlet 

channel clean out
11

o Seeding of wild rice in appropriate habitats

o Invasive species control (including carp, cattail, purple loosestrife, 

and Eurasian watermilfoil) where these species are impacting 

wildlife habitat using fish barriers, biocontrols, pesticides, and 

herbicides

o Predator fish stocking to manage benthivorous and planktivorous fish 

species (needs to be combined with other management strategies)

o Establishing Migratory Waterfowl Feeding and Resting Areas

(MWFRAs), Refuges and Sanctuaries to minimize waterfowl 

disturbance

o Establishing motorized surface use restrictions to reduce waterfowl 

disturbance and/or prevent damage to aquatic habitats

Watershed Management

o Wetland and grassland restoration and/or protection through fee title 

acquisition, conservation easements through non-profits and farm 

bill programs, and special efforts like the Working Lands Initiative

o Improved watershed management through controlled drainage and 

promoting other Best Management Practices (BMPs)

o Management of wetlands and lakes connected to Designated Wildlife 

Lakes, and lakes with adjacent public land

Target 2a: By 2030, actively manage as many of the shallow lakes 

completely within WMAs and all the DWLs for high quality waterfowl habitat 

as feasible. Work cooperatively with the FWS and other partners to increase 

active management of shallow lakes and other water bodies within WPAs and 

NWRs. Table 2 provides a summary of numbers and distributions of these 

lakes.

Implementation

A map and list of shallow lakes completely contained within WMAs, WPAs 

and/or NWRs is included in Appendix A 

10 WMA/WPA/NWR basins will be surveyed every year (under Objective

1)

Management or protection of 33 new basins under Objectives 2-5 needs 

to be accomplished annually; a portion of those would come from this 

category 

Overall annual goals for Objectives 2-5 include:

o50 basins identified for feasibility studies

o20 basins identified for wild rice designation

o10 basins receiving new or replacement water control structures 

Target 2b: Increase grassland and wetland restoration and protection of native 

habitats in the direct contributing catchment basins of these important lakes. In 

this case the direct catchments are targeted to improve complexes of wetlands 

and grasslands near shallow lakes to improve breeding duck habitat. Spreading 
12

these efforts across the entire watershed would not result in great habitat 

improvement and it would be also difficult to do on a scale that would improve 

water quality.

Implementation

Coordinate and support implementation of grassland and wetland

restoration objectives in the Duck Plan

Objective 2 Operational Plan:

Coordinate with Regional and Area Wildlife staff to identify 1-2 new 

projects per work area per year

Four additional specialists to handle project logistics in NE, NW, and 

metro/central Minnesota

One dedicated realty specialist to work on easements and acquisitions for 

shallow lake and wildlife projects

Include shallow lake management targets in work plans of Area Wildlife 

staff

Work with the DNR Division of Waters to delineate catchments of basins 

between 50 and 100 acres in size (those shallow lakes that have not had 

catchments yet delineated)

Make the priority shallow lakes GIS coverage available on network servers 

(on DRS)

Incorporate priority shallow lake catchment scoring criteria into the DNR 

WMA acquisition process 

Coordinate with other agencies implementing conservation to facilitate 

consideration/priority of land and wetlands within priority shallow lake 

catchments (facilitate habitat complexes adjacent to shallow lakes). Work 

in watersheds would also be beneficial from a water quality perspective.

Objective 3: Maximize management of shallow lakes for waterfowl and wildlife 

that are adjacent to public lands managed specifically for wildlife or public lands 

with wildlife habitat value.

Justification: Shallow lakes with a portion of their shorelines surrounded by 

public lands that are valuable for wildlife should also have high quality habitat. 

Only a few of these lakes are currently managed, and many additional 

opportunities for increased management and habitat improvement exist. The 

shallow lakes located partially within these areas of public ownership have some 

protection from shoreline development and may have large areas of upland 

buffers. This protection, however, has not insured that these basins have 

maintained the ecological functions of high quality shallow lakes with good

wildlife and waterfowl habitat and water quality. As with other shallow lakes, 

many of the lakes adjacent to these areas of public ownership have also suffered 

from invasive fish species, excessive nutrient loading, high water levels and 

climate change. Managing these lakes adjacent to public lands is also consistent 
13

with the goals in the Duck Plan, as shallow lakes are key components to habitat 

complexes of grasslands and wetlands.

Throughout the forested areas of Minnesota and much of the transition zone, the 

best waterfowl habitat is contained in wild rice lakes. Many wild rice lakes are 

plagued by high, stabilized water levels due to the installation of dams. These 

dams were put in after the drought of the 1930’s and have been especially 

damaging to wild rice during the above average precipitation Minnesota has 

experienced since the early 1990’s. Beaver dams have also been damaging to 

the state’s wild rice resource. The current joint DNR-Ducks Unlimited wild rice 

management project has proven that removal of these dams is a cost-effective 

management strategy, and these efforts should continue. Abundant wild rice has 

benefited many species of wildlife including muskrats and other furbearers on 

some of these lakes. Recommendation 6 in the DNR’s 2008 Wild Rice Study 

Legislative Report also supports additional wild rice management.

There are 25 shallow lakes completely within or have shoreline contained within 

State Parks or State Recreation Areas (with no other public land adjacent to 

them). These lakes provide valuable habitat for native wildlife and flora and 

recreational and educational opportunities for the public. Additional management 

opportunities may exist on these lakes. Such management would be a joint effort 

between the Division of Fish and Wildlife and the Division of Parks and Trails and 

would be consistent with overall management plans and goals of the particular 

park and the Minnesota State Parks Strategic Plan. 

Since these lakes have adjacent upland habitat, they are already forming a 

habitat complex and should receive higher priority for active management. 

However, they also have portions of shoreline in private ownership. Wildlife Lake 

Designation, flowage easements, or fee-title acquisition from willing sellers will be 

required in order for active water level management to occur on these basins. 

Since these lakes have a portion of their shorelines under private ownership, 

increasing public awareness of shallow lake ecology and management will be a 

critical component of implementing management on these lakes. Landowner and 

public buy-in will be essential for obtaining legal control for water level 

management activities. 

There may be some opportunities for wildlife management on basins formerly 

used by the DNR Section of Fisheries Management (Fisheries) as “Northern Pike 

Spawning Areas.” These are usually smaller wetlands or shallow lakes with 

connections to larger fishing lakes where Fisheries acquired land or easements 

for the purposes of creating or enhancing northern pike spawning habitat. There 

are approximately 18 Northern Pike Spawning Areas on shallow lakes. Fisheries 

is no longer actively managing many of these areas, and management of at least 

two have already been turned over to the Section of Wildlife Management for 

waterfowl and wildlife management purposes.
14

Primary Strategies

In-Lake Management

o Water level management including installation of permanent water 

control structures or use of temporary pumps or siphons 

o Rotenone treatments to manage fish populations

o Maintenance of water levels through beaver dam removal and outlet 

channel maintenance

o Seeding of wild rice in appropriate habitats

o Invasive species control (including carp, cattail, purple loosestrife, 

and Eurasian water milfoil) where these species are impacting 

wildlife habitat using fish barriers, biocontrols, pesticides and 

herbicides 

o Predator fish stocking to manage benthivorous and planktivorous fish 

species

o Establishing MWFRAs, Refuges and Sanctuaries to minimize 

waterfowl disturbance

o Establishing motorized surface use restrictions to reduce waterfowl 

disturbance and/or prevent damage to aquatic habitats and control 

internal nutrient loading

Watershed Management

o Wetland and grassland restoration and/or protection through fee title 

acquisition, conservation easements through non-profits and farm 

bill programs, and special efforts like the Working Lands Initiative

o Improved watershed management through controlled drainage and 

promoting other Best Management Practices (BMPs), including 

BMPs in managed forests

Public Awareness

o News releases highlighting shallow lake management projects

o Informational and educational videos

o Provide information through the Shallow Lakes web page on the 

DNR website

o Explore opportunities for interpretive displays on shallow lake

ecology at State Parks

o Continue support of the Shallow Lake Forum and other meetings and 

conferences

o Prepare articles for the Conservation Volunteer and similar 

publications

o Shallow lake brochures

o Presentations at lake association meetings, waterfowl symposiums, 

and special workshops

Target 3a: By 2056, actively manage the majority of the 1,553 shallow lakes 

with a portion of their shorelines under state, federal, or county ownership 

(WMAs, State Forests, State Parks, WPAs, NWRs, county lands) for high

quality wetland wildlife habitat with special emphasis on waterfowl habitat.

Management of shallow lakes associated with State Parks also falls under 
15

this goal; however, management on these basins needs to consider the 

management goals of the individual state park. It is expected that there 

would be goals that would be mutually beneficial to both the Division of Parks

and Trails and the Section of Wildlife Management. Management emphasis 

in the prairie and transition zones will be on water level management and/or 

biomanipulation and protecting those lakes that are in good condition.

Increased wild rice enhancement and protection will be emphasized in the 

forested areas of the state. Management of terrestrial vegetation around 

shallow lakes in forested lands owned by the DNR is guided by DNR 

Subsection Forest Resource Management Plans (SFRMPs). This Shallow 

Lakes Program Plan is not intended to replace or change the existing SFRMP 

process. Table 2 provides a summary of numbers and distributions of these

lakes.

Implementation

A map of shallow lakes adjacent to (but not completely contained within) WMAs, 

WPAs, NWRs, State Forests and county lands is included in Appendix A. 

40 lakes from this list will be surveyed every year

15 management plans will be developed every year

Management and/or protection of 33 new basins under Objectives 2-5 

needs to be accomplished annually in order to achieve the target of 1,800 

managed lakes by 2056; a portion of those would come from this 

category.

Target 3b: Designate an additional 30 lakes as wildlife management lakes 

under M.S. 97A.101

Implementation

Start the 97A.101 designation process on 4-6 lakes per year.

Complete the designation process on 2-3 lakes (with parts of their 

shorelines already under public ownership) per year as wildlife 

management lakes under M.S. 97A.101, achieving designation of at least 

an additional 30 lakes in 10 years.

Basins targeted for designation will have high management potential and 

high likelihood of achieving desirable habitat conditions after management 

(e.g. lakes with small watersheds and few connections).

Target 3c: Increase grassland and wetland restoration and protection of 

native habitats in the direct contributing catchment basins and along the 

shorelines of these lakes in the prairie and transition zones.

Implementation

Support implementation of grassland and wetland restoration objectives in 

the Duck Plan.
16

Coordinate targeting of restoration and protection in shallow lake 

watersheds.

Target management of lakes in prairie and transition regions that are, or 

can be, parts of habitat complexes of wetlands and grasslands.

Use GIS tools and work with Area Wildlife staff to identify lakes that have 

the potential to be managed as a part of a habitat complex of grasslands, 

wetlands or native habitats

Target 3d: Protect waterfowl habitats in shallow lakes in forested areas.

Implementation

Work with partners to protect shorelines of important wild rice lakes 

through conservation easements.

Work with other Divisions on formulating management plans for forested 

shallow lakes. Such plans would usually focus on in-lake management 

techniques and motorized surface use management, but would also 

encourage best management practices in the upland areas.

Acquire shoreline habitats on important wildlife lakes through fee-title 

acquisition.

Identify specific opportunities for shallow lake management projects in 

state forests.

Target 3e: Increase public knowledge and understanding of shallow lake 

ecology and management.

Implementation

A minimum of 5 news releases on shallow lake projects will be put out 

annually

Additional information and education materials including brochures and 

videos will be produced and distributed.

The DNR Shallow Lakes Program website will be maintained.

Public presentation opportunities will be sought out.

Involvement in the Shallow Lakes Forum will continue.

Operational Plan

Coordinate with Regional and Area Wildlife staff to identify 1-2 new 

projects per work area per year.

Four additional specialists to handle project logistics in NE, NW and 

metro/central Minnesota.

One dedicated realty specialist to work on easements and acquisitions for 

shallow lake and wildlife projects.

Include shallow lake management targets in work plans of Area Wildlife 

staff.
17

Wildlife managers will coordinate with the Division of Forestry on potential 

shallow lake management through the Interdisciplinary Forest 

Management Coordination Framework.

The Shallow Lakes educational brochure will be updated through the 

Shallow Lake Forum.

Each Shallow Lake Program staff member will be required to do at least 

one educational/informational presentation annually.

The DNR Shallow Lakes Program website will be updated monthly.

News releases will be done on all new lake management projects.

Local Shallow Lake Program staff specialists will do news releases 

annually on local shallow lake condition and project updates.

Maintain existing Shallow Lake Program staff level commitment to this 

activity.

Each Shallow Lake Program specialist can realistically complete one 

designation per year with help from Area Wildlife staff.

Coordinate with Regional Wildlife staff and Shallow Lake Program staff to 

further prioritize lakes for designation.

Make the priority shallow lakes GIS coverage available on network servers 

(on DRS).

Incorporate priority shallow lake catchment scoring criteria into the DNR 

WMA acquisition process.

Coordinate with other agencies implementing conservation to facilitate 

consideration/priority of land and wetlands within priority shallow lake 

catchments (facilitate habitat complexes adjacent to shallow lakes).

Work with the Wild Rice Work Group to identify wild rice lakes in need of 

protection through conservation easements or fee title acquisition.

Objective 4: Increase waterfowl and wildlife habitat in shallow lakes with public 

access that do not have tracts of shoreline specifically managed for wildlife. 

Justification:

There are 201 shallow lakes with public access but without other adjacent 

public wildlife lands. Many of these lakes are managed for game fish 

populations, but some also have waterfowl habitat and provide public hunting 

opportunities. Some of these lakes are designated Migratory Waterfowl 

Feeding and Resting Areas (MWFRAs) but are also managed as recreational 

fisheries. Currently most do not have formal wildlife management plans or 

joint fisheries and wildlife management plans. Many do not have lake habitat 

assessments. Many of these lakes are in areas of the state where all the 

lakes are shallow, thus both fisheries and wildlife management goals need to 

be considered. Fisheries and Wildlife should coordinate survey efforts to 

have a basis of information for these lakes that could be used for formulating 

joint management strategies. Because only a small portion of the shoreline of 

these lakes may be under public ownership, additional steps will be required if

active water level management is appropriate on a lake-by-lake basis. Some 
18

shallow lakes adjacent to public lands are currently managed for recreational 

fishing but still provide valuable waterfowl habitat. It is critical that wildlife 

habitat needs are also addressed in the management plans for these lakes. 

The same tools used on lakes with partial public ownership of shoreline can 

be used to manage lakes without adjacent public land beyond the public 

water access site. Public support of proposed management actions will be 

critical on these lakes, and active water level management will likely be 

controversial due to perceptions that aquatic vegetation is not desirable on 

many lakes. Management with sport fish/predator fish may be a component 

of management plans, since many of these lakes are already managed for 

sport fisheries. While it may be difficult to meet multiple goals associated with 

managing for both fish and wildlife habitats and uses, there are examples of 

successful joint management plans on shallow lakes in Minnesota (Fulda, 

Scotch, and others) and from other states (Big Muskego, Wisconsin).

As with Objective 3, increased public awareness of shallow lake issues and 

management techniques will be important to build public support for projects 

under Objective 4. News releases, informational publications and videos, 

Shallow Lake Forums, and presentations at various meetings (Minnesota 

Waterfowl Association, Minnesota Waters conferences, water quality 

workshops, watershed districts) will be utilized. As the public becomes more 

aware of shallow lake problems and tools to address those problems, 

acceptance of active management of these lakes will increase.

Primary strategies

In-Lake Management

o Water level management including installation of permanent water 

control structures or use of temporary pumps or siphons.

o Wildlife Lake Designation or other legal processes in order to 

manage water levels.

o Rotenone treatments to manage fish populations.Maintenance of 

water levels through beaver dam removal and outlet channel 

maintenance.

o Seeding of wild rice in appropriate habitats.

o Invasive species control (including carp, cattail, purple loosestrife, 

and Eurasian watermilfoil) where these species are impacting 

wildlife habitat using fish barriers, biocontrols, pesticides, and 

herbicides.

o Predator fish stocking to manage benthivorous and planktivorous fish 

species (predator fish selected for ecological conditions found in 

shallow lakes).

o Establish MWFRAs, Refuges and Sanctuaries to minimize waterfowl 

disturbance.

o Establish motorized surface use restrictions to reduce waterfowl 

disturbance and/or prevent damage to aquatic habitats.
19

o Local ordinances to protect shorelines or enact surface use 

restrictions.

Watershed Management

o Wetland and grassland restoration and/or protection through fee title 

acquisition, conservation easements through non-profits and farm 

bill programs, and special efforts like the Working Lands Initiative.

o Improved watershed management through controlled drainage and 

promoting other Best Management Practices (BMPs)

o Partnerships with other entities doing watershed work (e.g. working 

forestry easements, watershed district efforts to improve water 

quality).

Public Awareness

o News releases highlighting shallow lake management projects.

o Informational and educational videos.

o Provide information through the Shallow Lakes web page on the 

DNR website.

o Continue support of the Shallow Lake Forums and other meetings 

and conferences.

o Prepare articles for the Conservation Volunteer and similar 

publications.

o Shallow lake brochures.

o Presentations at lake association meetings, waterfowl symposiums, 

and special workshops

.

Target 4a: Increase management efforts to benefit wildlife on the 201 shallow lakes 

with public access but without large tracts of public land managed for wildlife 

adjacent to shorelines. Table 1 provides a summary of numbers and distributions of 

these lakes.

Implementation

5 lakes from this list will be surveyed every year. Wildlife lake surveys 

should be coordinated with Fisheries surveys, as it would be beneficial to 

have both fisheries assessments and wildlife assessments from the same 

year.

Develop joint Wildlife and Fisheries management plans for those lakes 

that are Migratory Waterfowl Feeding and Resting Areas and are

managed for game fish.

All management plans, including Comprehensive Lake Management 

Plans and Lake Vegetation Management Plans, developed for all lakes 

with public access should be reviewed through an interdisciplinary process 

by both Wildlife and Fisheries staff at Area and Regional levels. Such 

review should occur early in the process of developing management 

strategies.

Target 4b: Use Wildlife Designation as a tool if primary management 

emphasis is for wildlife and waterfowl management.
20

Implementation

Identify shallow lakes that have public access with no additional public 

land and are not currently managed by Fisheries but may have wildlife 

management potential.

Operational Plan

In order to implement this piece of the plan, a specific policy is needed.

Proposed Policy: Lake management plans for shallow lakes developed by the 

Division of Fish and Wildlife for any purpose will be subject to interdisciplinary 

review and comment at the area and regional level by both the Fisheries and 

Wildlife Management Sections prior to approval by the respective Section Chief. 

Note: management plans for Designated Lakes currently are reviewed and 

approved by the Division Director.

Rational: Existing policy requires a coordinated review by DNR Fisheries and 

Wildlife staff for aquaculture license applications and the use of wetlands for fish 

rearing purposes. This coordination is carried out at the area level with regional 

and central office involvement as necessary. The benefit of this coordination 

should be extended to lake management plans for shallow lakes regardless of 

the primary management focus.

This review and comment policy would reduce potential conflicts (for example, 

when a lake with a Migratory Waterfowl Feeding and Resting Area is managed 

as a recreational fishery), provide a united defense of plans, and foster additional 

joint Fisheries and Wildlife management plans. Wildlife currently requests 

Fisheries review of management plans developed during the Wildlife Lake 

Designation process.

Shallow Lake Program staff will request review of Fisheries management 

plans on these 201 shallow lakes that are managed as recreational 

fisheries.

Development of joint Fisheries and Wildlife management plans will be 

requested on a case-by-case basis except for those lakes that are also 

Migratory Waterfowl Feeding and Resting Areas.

Fisheries and Wildlife staff will develop joint management plans on 

MWFRA lakes that are managed as recreational fisheries through a 

specific process including Area, Regional and Central Office staff.

The Shallow Lakes educational brochure will be updated through the 

Shallow Lake Forum.

Each Shallow Lake Program staff member will be required to do at least 

one educational/informational presentation annually.

The DNR Shallow Lakes Program website will be updated monthly.

News releases will be done for all new lake management projects.
21

Local Shallow Lake Program specialists will do news releases annually on 

local shallow lake conditions and project updates.

Forest Transition Prairie Total

Total number of shallow lakes 1216 1462 1391 4069

Priority Shallow Lakes

Objective 2

Designated Wildlife Lakes 6 15 23 44

Completely within WPAs 0 2 15 17

Completely within NWRs 17 16 8 41

Completely within WMAs 21 51 15 87

Completely within State Parks 4 5 2 11

Objective 3

Partially in WMAs 88 213 307 608

Partially in WPAs 2 52 170 224

Partially in NWRs 2 23 0 25

State Forest and County lands 563 105 14 682

Partially in State Parks 3 8 3 14

Objective 4

Public Access, no additional public land 43 69 89 201

Total 749 559 646 1954

Table 1. Shallow Lakes by Ecoregion, Program Plan objectives and public land 

category. The total number of lakes exceeds the 1800 statewide target, and this 

list will change as patterns of public land ownership change. Given that there will 

be limitations preventing management of all of these lakes above, the additional 

lakes will provide managers some discretion on which to manage while still 

achieving the goal.

Objective 5: Increase awareness and protection of lakes containing measurable 

stands of wild rice.

Target 5: Identify and maintain a list of “Important Natural Wild Rice Areas” as 

recommended in the 2008 Wild Rice Study Legislative Report.

Justification:

Wild rice is an important waterfowl and wildlife resource. The 2008 report on wild 

rice specified the state would identify and publish a list of important natural wild 

rice areas. While this listing will not offer any direct protection or additional legal 

authority for active management, it will increase awareness of the value of wild 

rice and give local governments an additional tool that could be used in 

conjunction with local ordinances to protect this valuable resource. The state 

provides the overall framework for shoreline management, but shoreline

ordinances are developed and administered locally. Often local governments 

lack specific information on a particular water body or natural resource. A list of 

the state’s most important wild rice areas, compiled from professional and public 

input, would call attention to the significance of these areas, provide local 

governments with information about a valuable resource in their local 
22

jurisdictions, and increase awareness among the public about these noteworthy

sites.

Primary Strategies

Identify and maintain a list of “Important Natural Wild Rice Areas”.

Publish the list on the DNR website and make it available to resource 

professionals, citizens, and local units of government.

Identification and listing provides information to local governments to 

enact additional protections of these lakes/areas through local ordinance. 

It also provides information to and increases awareness among citizens.

Implementation

The interagency Wild Rice Work Group established through the 

recommendation of the 2008 Wild Rice Study Legislative Report will work 

to establish criteria for important wild rice lakes. The DNR Shallow Lakes 

Program will work through the Work Group, DNR Wildlife staff, and 

stakeholders to identify a list of lakes that meet the criteria for listing as 

important wild rice areas. 

Wild rice distribution and lakes managed for wild rice are illustrated in 

Appendix A. 

Operational Plan

A Wild Rice Work Group (WRWG) is already established to develop 

recommendations and collaborate on wild rice issues, including managing

wild rice, encouraging wild rice harvesting, and increasing public 

awareness of the importance of wild rice.

The WRWG and sub-work group committees need to meet regularly and 

establish goals with specific timelines.

A Shallow Lakes Program specialist currently serves on these committees 

which provide input and recommendations for identifying and listing

“Important Natural Wild Rice Areas”.

Develop a specific public input process (work with SORA and the Native 

American Bands) to identify and list “Important Natural Wild Rice Areas”.

Target for start of process: January 2011.
23

BACKGROUND 

Basic Shallow Lake Ecology and Management

The following background is provided to put the proposed management of shallow lakes 

in this plan into a scientific, ecological, and wildlife habitat context. The science of 

shallow lake ecology is a relatively new area of study. Only in the last 20 years has 

shallow lake ecology become a distinct topic within the broader fields of limnology and 

ecology. 

Key to understanding and managing shallow lakes is defining what makes them unique 

from deep lakes. Deep lakes thermally stratify, or separate into layers based on water 

temperature, during the summer months. The epilimnion, the layer nearest the surface, 

is isolated for most of the summer from the nutrients contained in the sediments of the 

lake bottom due to this stratification. Shallow lakes do not form stable, distinct thermal 

layers during the summer months. The water column is mixing throughout the summer, 

and there is exchange of nutrients between the water and lake sediments (Scheffer 

2004). This frequent water-sediment interaction results in a nutrient rich environment. 

A shallow lake compared with a deep lake of the same size and same watershed is 

going to have higher nutrient concentrations.

Another difference between shallow and deep lakes is the abundance and importance 

of aquatic plants. Aquatic vegetation growth is limited to the shallow areas of deep 

lakes, but aquatic plants can grow over the entire bottom in a shallow lake. Because 

aquatic vegetation can have such extensive coverage in these lakes, it is a key 

component of a shallow lake ecosystem. 

There is evidence that shallow lakes can exist in either of two conditions: one of clear 

water and abundant vegetation or one of turbid water, little or no aquatic vegetation but 

abundant algae. Such shifts in condition can also occur in deeper lakes, but are not as 

evident as in shallow lakes. Each state is relatively stable depending upon nutrient 

concentrations. In the clear water state, aquatic plants serve to keep the water clear by 

protecting sediments from wind-resuspension, providing habitat for filter-feeding 

invertebrates and storing nutrients. Lakes in the clear water condition also support a 

greater diversity of wildlife and waterfowl. In the turbid water condition, algae and 

suspended sediments prevent the growth of aquatic plants and the water stays turbid. 

Lakes in this turbid condition provide little or no habitat for wildlife and waterfowl.

Many shallow lakes are in the turbid condition due to eutrophication caused by changes 

in watersheds of lakes that increases external nutrient loading. Changes in the fish 

community of a shallow lake can also cause deterioration from clear water to turbid 

water. Lakes dominated by bottom feeding fish and other planktivorous fish tend toward 

the turbid water condition. Bottom feeding fish (carp, bullheads) stir-up bottom 

sediments and uproot aquatic vegetation but more importantly increase internal nutrient 

loading through their metabolic activities (Brabrand et al. 1990, Persson 1997, Zimmer 

et al. 2006). Planktivorous fish consume small invertebrates that filter feed on algae. 
24

These invertebrates can filter enough algae out of the water at times to have impacts on 

water clarity.

Due to stabilizing interactions, once a lake is in the turbid condition it is difficult to 

restore a clear water regime and watershed management alone may not be to reverse 

the lake back to the clear water condition. Additionally, in large watersheds, it is not 

feasible to restore pre-settlement conditions to the extent that would be required to see 

noticeable changes in habitat quality in a lake. Some type of in-lake management is 

required to change the cycling of 

nutrients already in the lake. 

Changing how nutrients are cycled in a 

lake and where they are stored

requires dramatic manipulations of the 

biological interactions occurring 

among fish, invertebrates and algae. 

Common techniques to switch a lake 

from the turbid to the clear state 

include drawdowns, changing the fish 

community through chemical 

treatments, predator stocking or 

through other means (winter 

drawdown). These manipulations 

allow a brief window of low fish 

abundance. Without predation 

pressure from fish, invertebrate 

populations flourish, grazing on algae

and improving water clarity, and 

allowing aquatic plants to grow. The 

plants then stabilize the clear water in 

the lake. If carp are present in the 

system, and are able to repopulate 

after a partial winterkill or incomplete 

kill from a chemical treatment, 

improvements in water clarity and 

habitat maybe short-lived. Partial 

winterkills can create reproductive 

opportunities for carp. They are able 

to have a successful year class in the 

absence of competition or predators 

(Bajer and Sorensen 2009). Such partial winterkills are common in shallow lakes, even 

those with aeration systems.

While biological interactions in shallow lakes can cause switches from the clear to the 

turbid state and vice versa, underlying nutrient levels in a lake also influence the 

likelihood that a lake will be turbid or clear. At low nutrient levels, a shallow lake is more 

likely to be clear, at mid-levels of nutrients a lake can switch between both states and at 

Figure 2. Shallow lakes are distributed through 

the forest, transition and prairie portions of the 

state.
25

high nutrient levels, a lake is more apt to have turbid water. Many things can influence 

the underlying nutrient levels in lakes, including watershed size, soil type, topography, 

and watershed development (Moss et al. 1997). Such factors need to be considered 

when choosing shallow lakes to manage and when formulating expectations from 

management. Those lakes with watersheds that have higher percentages of native 

vegetation and intact wetlands should be high priority for protection (both lake and 

watershed). Lakes with impacted watersheds are going to require more aggressive inlake management and also restorative measures in their watersheds. Even with 

aggressive management, it may be difficult to maintain high water clarity in some lakes, 

although improvements in habitat are likely possible. For example, active management 

of a highly eutrophic system may not result in long-term improvements in water clarity, 

but increases in tolerant species of aquatic plants (ie sago pondweed) maybe 

attainable. In those cases, repeated management would be necessary to maintain 

habitat.

Shallow Lakes in Minnesota

Resource Base

Minnesota has a resource of over 4,000 shallow lakes (Figure 2). The majority of these 

lakes fall between 50 and 100 acres in size; 115 are over 1,000 acres, and nearly 50 

exceed 2,000 acres. These shallow lakes are 50 acres or greater in size and have a 

maximum depth of 15 feet or less. Examples of large lakes include Minnesota’s most 

famous waterfowl hunting lakes such as Swan Lake in Nicollet Co. (9,346 acres), Heron 

Lake in Jackson Co. (8,251 acres), 

Lake Christina in Douglas Co. (3,978 

acres), Pelican Lake in Wright Co. 

(2,793 acres), Thief Lake in Marshall 

Co. (7,430 acres) and Big Rice Lake in 

Cass Co. (2,717 acres). Approximately 

1,700 shallow lakes have been drained 

prior to the 1970’s, and most of those 

remain drained. Table 2 provides a 

summary of general information on 

numbers and uses of shallow lakes in 

Minnesota.

While shallow lakes are distributed 

throughout the state (Fig. 2), habitat 

characteristics vary among and within 

regions. Habitat and water quality tend 

to be poor where watersheds have 

been dramatically altered by 

agricultural or urban development. 

Figure 3. Red dots lakes in poor 

condition, blue dots indicate lakes in 

good condition
26

Data from DNR shallow lake surveys (Figure 3) suggest that the majority of prairie 

region shallow lakes have poor water clarity and consequently poor conditions for 

submerged aquatic plants and invertebrates, the primary sources of food for migrating 

and breeding ducks. 

Total Existing Shallow Lakes, or lakes 50 acres or 

greater in size with maximum depths of 15 feet or 

less 

(there are still many lakes with unknown/unrecorded water 

depths)

~4069

Shallow Lakes fully drained or partially drained

(according to Bulletin 25)

1752

Designated Wildlife Lakes under M.S. 97A.101 (2010) 44

Shallow Lakes Managed for Game Fish 754

Shallow Lakes Used for Aquaculture 199

Shallow Lakes associated with public lands (State, 

Co. and USFWS)

1709

Shallow Lakes with public access but no other public 

land

201

Shallow Lakes with Wild Rice 559

Shallow Lakes with MWFRAs 37

Table 2. General shallow lake information. There is overlap in lakes in each 

category, for example, wild rice lakes may also be counted in lakes associated 

with public lands, or a Designated Wildlife Lake could also have a MWFRA.

Importance of Shallow Lakes for Waterfowl 

Quality shallow lakes are critical habitats for waterfowl production and migration. These 

lakes play two important roles in waterfowl production. The first is providing abundant 

energy in the form of aquatic invertebrates for breeding hens. These invertebrates are 

most important for diving ducks, particularly lesser scaup. The second contribution is in 

providing high quality duckling brood habitat. High quality brood habitat leads to 

increased ducking survival rates and duckling survival is a critical component to 

improving the duck recruitment rate.

Emergent aquatic plants such as rushes, wild rice and rooted common cattail enhance 

brood habitat by providing protective cover from weather and predators, and by 

providing habitat for aquatic invertebrates. Aquatic invertebrates such as insects, 

amphipods and snails are critical for duckling growth and survival. An abundance of 

invertebrates reduces the time ducklings spend foraging, which increases their survival 

rates. The quality of shallow lakes providing brood habitat has dramatically declined due 

to a combination of factors including prolonged periods of high water that favor winter 

survival of undesirable fish, such as bullheads and carp. These fish reduce the 

invertebrates and aquatic plants necessary for brood survival (Buoffard and Hanson 

1997, Hanson and Riggs 1995).
27

Ducks are driven by their need for food and rest during fall migration. Temporary and 

seasonal wetlands sometimes fill these needs for dabbling ducks during extremely wet 

falls, particularly within the prairie region of the state. However these ponds are usually 

dry during the average fall. Typically it is the larger, more permanent wetlands and 

shallow lakes that provide the most important fall habitat. Unfortunately in Minnesota,

the quality of this habitat has declined markedly due to shoreline development, 

drainage, excessive runoff, sedimentation, and dominance by invasive plant and fish 

species. 

The worst damage has occurred within the prairie and transition portions of the state 

(Figure 3). The impacts of wetland drainage are multifold including direct loss of habitat 

for wetland dependant species, increased nutrients and siltation in remaining wetlands 

and lakes, altered hydrology including loss of flood storage, increases in water levels 

and altered food webs (Blann et al. 2009). Subsurface drainage tile also can divert 

ground water into surface drainage, further adding water that normally go to ground 

water recharge to these systems (Leopold 1968 and Skaggs et al. 2005). Restoration of 

wetland and grassland complexes within the watersheds of these lakes will help reduce 

excessive runoff and improve water quality in the long-term. However watershed work 

alone will not resolve in-lake degradation problems nor restore invertebrate populations 

related to high populations of undesirable fish species including carp and bullheads. It is 

not completely understood how much conservation and management will be needed to 

show improvement in the condition of aquatic systems in these impacted landscapes 

(Blann et al. 2009)

Importance of Shallow Lakes to Other Wildlife and Species of 

Greatest Conservation Need

Shallow lakes provide important habitat to many environmentally sensitive species and 

species listed as having the “Greatest Conservation Need” by the MnDNR in 

Tomorrow’s Habitat for the Wild and Rare (THWR). Over 20 species listed as a species 

of greatest conservation need (SGCN) utilize shallow lake habitats (MnDNR 2006). 

They include many water bird species that nest on shallow lakes including grebes and 

terns. Their habitats have been negatively impacted by loss of emergent vegetation or 

increases in water level bounce caused by change in watersheds or lake outlets. 

Shorebirds also utilize shallow lake habitat, especially those that are in a natural or 

managed drawdown during their migration. Several species of frogs, toads and turtles 

are also found in shallow lakes. 

Shallow lakes were listed as “key habitats for species of greatest conservation need” 

specifically in six of the state’s 25 ecological subsections. Those six subsections were 

located in the Prairie Parklands and Eastern Broadleaf Forest provinces. Management 

options to support SGCN in the report include preventing loss and degradation of 

shallow lakes, focus on protecting larger shallow lakes and wetland complexes, manage 

for natural water regimes in shallow lakes, manage infestations of invasive plants and 

animals in shallow lakes, and protect known nesting areas for Forster’s terns. 
28

Shallow Lakes and Wild Rice

Minnesota ranks first in the nation among states for natural wild rice production. While 

not all wild rice lakes are shallow lakes, Minnesota has over 1,000 (Figure 4) lakes 

containing stands of wild rice; over half of these are shallow lakes. Wild rice provides 

important brood and migration habitat for ducks in the forest and portions of the 

transition zone. Many of these wild rice stands have deteriorated due to high water 

caused by lake-outlet blockages by beaver dams and dense growths of hybrid or 

narrow-leaf cattail. Managing wild rice remains an ongoing project for the DNR. In 

recent years, Ducks Unlimited, tribal governments, and lake associations have been 

important partners in these efforts. 

Wild rice stands are also susceptible to damage by shoreline development. Over the 

last 20 years, housing density has increased in both the forest and transition areas of 

the state and growth was greatest in counties with abundant forests and lakes 

(Gustafson et. al. 2005.). This area is also the part of the state with the most wild rice 

habitat. A recent study found an average of 66% loss of aquatic vegetation along 

developed shorelines (Radomiski and Goeman, 2001). Many counties with the bulk of 

the state’s wild rice lakes (Figure 4) are also expected to receive the brunt of a 24% 

increase in Minnesota’s population by 2035 (Figure 5). 

Figure 4. Wild rice distribution
29

Waterfowl Hunting and Wildlife/Waterfowl Viewing

Despite substantial losses in the quantity and quality of the state’s shallow lakes, 

Minnesota remains one of the most important waterfowl production and harvest states 

in the Mississippi Flyway. Minnesota typically fields over 100,000 waterfowl hunters and 

400,000 waterfowl watchers/birders a year, one of the highest in the nation. Annual trip 

and equipment expenditures by these enthusiasts in 2001 totaled more than $224

million and generated more than $20 million in state tax receipts.

Declines in shallow lake quality directly affect waterfowl hunting opportunities. Places to 

hunt and waterfowl to see are critical elements leading to hunter satisfaction (Schroeder 

et al. 2007). Restoring and protecting the habitat needed by migrating ducks is 

obviously beneficial for hunters as well. Access to some shallow lakes can be physically 

intimidating for many hunters and impossible for those challenged by age or physical 

ability. Balancing the issue of increased disturbance with appropriate access will be a 

challenge for the DNR, particularly as the population ages.

Figure 5. Projected population change by 

county.
30

SHALLOW LAKE MANAGEMENT FOR WILDLIFE

In Minnesota, there are approximately equal numbers of shallow lakes in the forest, 

transition and prairie areas (Figure 2), but the characteristics and conditions of the lake 

resources differ considerably among the ecological zones. Management strategies 

must differ accordingly.

Many of the shallow lakes of 

the prairie and western 

portions of the transition zone 

are large semi-permanent 

and permanent water bodies 

dominated by cattails and 

bulrushes along the 

shorelines and dense stands 

of submerged food plants, 

such as sago pondweed, 

throughout the basins. 

Reflecting the rich prairie 

landscape, the lakes are 

inherently nutrient-rich and 

can support an abundance of 

invertebrates and food plants. 

The quality of waterfowl 

habitat in prairie lakes is 

highly influenced by water 

clarity, abundance of aquatic 

plants and invertebrates. 

Often, excessive nutrients 

and undesirable fish can 

cause degradation of water 

clarity and these lakes shift to 

turbid, algae-dominated 

basins with few plants and invertebrates. Lakes in this condition have little value for 

waterfowl. Historically, frequent winterkills, low water cycles, and isolation from other 

water bodies, limited fish populations and maintained good quality habitat in prairie 

lakes and wetlands. 

Productivity of lakes and soils decreases as one moves north and eastward in the state. 

Lakes in the forested area of the state are less likely to have problems with excessive 

nutrient inputs. This area has also been less impacted by wetland drainage. The best 

waterfowl lakes in the forest are wild rice lakes. As mentioned earlier, wild rice stands 

provide important brood and migration habitat for waterfowl, but many of these wild rice 

stands have deteriorated due to high water caused by lake-outlet blockages by beaver 

dams and other obstructions. Managing wild rice is an ongoing project for the DNR and 

Figure 6. Lakes Designated as Wildlife Management Lakes 

under M.S. 97A.101
31

other partners, including Ducks Unlimited, tribal governments, and lake associations. 

For example, in 2007, over 170 lakes were 

managed for wild rice.

One of the primary tools the DNR has 

available for shallow lake management for 

wildlife is Lake Designation through 

Minnesota Statute (M.S.) 97A.101. This 

statute allows lakes to be designated 

specifically for wildlife management through 

a formal public hearing process. Such 

designation provides DNR wildlife 

managers with authority to manage water 

levels and control motorized use. Only 44

(Figure 6) of the more than 4,000 shallow 

lakes have been formally designated for 

wildlife management through this process. 

In comparison, about 754 shallow lakes 

have or are managed for recreational 

fishing in Minnesota by DNR Fisheries. An 

additional 199 lakes are licensed for private 

aquaculture activities. The lakes with 

recreational fisheries are evenly distributed 

throughout the state, but most of shallow 

lakes used for aquaculture are located in 

the prairie and transition areas of the state 

(Figure 7).

Figure 7. Shallow lakes with recreational 

fisheries or with aquaculture use. 
32

THE CHALLENGES

The problems plaguing shallow lakes occur at several management scales ranging from specific lakes to 

landscape levels. Table 3 highlights these problems in light of these different scales. Some of these 

issues are explored further in the following text.

Problem:

Scale of Impacts at: Possible Management 

Tools/Strategies In-Lake Shoreline Watershed Landscape 

Lack of 

Information 

Unknown Lake 

Condition 

Contribution of 

groundwater/wa

ter tables

development 

Thresholds 

trigger in-lake 

habitat decline

Extent of 

impact

Sources of 

greatest 

stressors

Unknown impacts of 

Climate and Land Use 

Changes 

Lake surveys

Additional research

Drainage Inventory

Ground water assessments

Long-term monitoring

Climate Change Lack of 

Winterkill 

Lakes drying 

up?

Increased algal 

growth

-- Increased 

Precipitation

Increased 

evaporation

Changes in water 

levels 

Changes in fish 

populations/communit

y structure, alterations 

to wet-dry cycles

Active management 

including water level 

manipulation and 

biomanipulation

Vulnerability assessments

Adaptive management

Land Use Increased 

sedimentation 

and nutrient 

inputs

Conversion of 

Natural 

Shoreline

Loss of 

Wetlands, 

Permanent 

Cover, 

increased 

runoff

Loss of Wetlands and 

Permanent Cover, 

increased runoff

Cost share/incentive 

programs for restoration 

activities

Conservation easements

Restoration of wetlands and 

grass lands

active in-lake management

Development Increase in 

nutrient inputs

Housing and 

Agriculture

Decreased 

habitat 

complexity

Housing and 

Agriculture

Loss of habitat Cost share/incentive for 

conservation easements

Direct protection through 

acquisition

Restoration, protection 

through conservation 

easements

Implementation of best 

management practices

Active lake management

Hydrological 

Alterations 

Outlet Changes

Irrigation

Industrial 

allocation

Ditches 

Drainage

Erosion

Vegetation 

changes

Increased 

Runoff

Loss of 

wetlands

Loss of 

isolation

Active water level 

management

Provide incentives for 

watershed restoration and 

restoration of historical 

hydrological regimes

Invasive Species Aquatic Plants 

and Animals

Aquatic and 

Terrestrial 

Plants

Change in ecological 

structure and function

Prevention: information and 

education, regulations 

Biomanipulation, active 

management including water 

level and herbicide or 

piscicide treatments

Physical 

Disturbance

Boating

Angling

Removal of 

near shore

vegetation

Regulatory including 

MWFRAs, surface use 

restrictions through 

Designation or local 

ordinance

Improved coordination of 

lake management between 

Fisheries and Wildlife

Competing Uses Aquaculture

Angling

Recreational 

boating

monocultures Decrease in diversity New aquaculture licensing 

criteria

Special regulations

Surface use restrictions

Vegetation management 

plans

Improved coordination of 

lake management plans 

between Fisheries and 

Wildlife

Table 3. Problems impacting shallow lake habitat at multiple scales and potential tools to address those 

problems.
33

Water Levels and Water Quality

More than a century and half of agricultural and urban development has taken its toll on 

Minnesota’s shallow lakes. The prairie area of the state is substantially drained with 

fewer than 10% of the original wetlands remaining; some shallow lakes were also 

drained. Row crops such as corn, soybeans and sugarbeets dominate the landscape. 

Runoff is much greater due to loss of wetlands and reduced soil porosity due to loss of 

perennial grass cover. Shallow lakes are often the receiving waters for much of this 

drainage and runoff. The result of decreased watershed storage and increase in 

drainage systems is lakes with more 

hydrological “bounce” in water levels

(flashy hydrographs) and increased 

levels of dissolved nutrients.

In addition to increased drainage, 

parts of the state have also 

experienced a trend of increased 

average annual precipitation in recent 

decades. Figure 8 shows how 

annual precipitation has increased in 

Otter Tail County in the last 20 years 

compared to the two decades prior. 

Similar patterns are evident in many 

other counties of the state. This 

increased precipitation has resulted 

in increased lake water levels. 

Deeper water combined with mild 

winters, earlier ice-out on lakes and 

increased connectivity (Figure 9) has decreased frequency of fish winterkill. Many of 

these lakes were important waterfowl lakes, but they now sustain game fish 

populations. Recent research predicts further reductions in the frequency and extent of 

winterkill in temperate lakes due to climate change. Duration, volume and temporal 

extent of anoxia are predicted to decrease in northern temperate lakes (Fang and 

Stefan 1997, 2000). When winterkills do occur, undesirable fish re-infest the lake 

quickly through enhanced drainage networks, thus increased connectivity from ditching 

and tiling in these systems has also led exacerbated degradation.

Increased numbers and types of fish in shallow lakes have added to water quality 

problems. Carp and other benthivorous fish increase nutrient levels in basins through 

their foraging activity and through excreted nutrients (Lougheed et al. 1998). These 

nutrients contribute to algal blooms that decrease water clarity and submerged aquatic 

plants. Research has clearly documented poor habitat quality in basins with high 

densities of undesirable fish, including such native species as black bullheads and 

fathead minnows (Hanson et al 2005, Herwig et al. 2006, Zimmer at al 2006). 

Figure 8. Precipitation data for Otter Tail County, MN 

from 1973-2009. Annual average by decade based on 

all available data in Otter Tail County from Minnesota 

State Climatology records. 
34

Increases in nutrients, higher water levels, suspension of bottom sediments, invasive 

species, algal blooms and shoreline disturbance have combined to eliminate aquatic 

plants and invertebrates and decrease water clarity and quality in many basins. Nearly 

two-thirds of the shallow prairie lakes surveyed by Minnesota DNR Shallow Lakes 

Program have poor water clarity and quality.

Continuing research has led to a better understanding of the intricacies of these 

relationships among fish, invertebrates, water clarity and lake nutrient levels. Although 

much remains to be learned, it is clear that lake management approaches cannot ignore 

biological interactions occurring in lakes if the management goal is related to waterfowl, 

fish or water quality. 

Invasive Species

Invasive fish, particularly carp, pose a serious challenge to maintaining water quality, 

desirable aquatic plants and invertebrates (Parkos et al. 2003). Documentation of 

problems with common carp in Minnesota date back at least to the 1940s and are 

generally limited to the southern half of the state (Sharp 1942). This fish was recognized 

as problematic in other parts of the country by the early 1900’s. Four new species of 

Asian carp that have not yet invaded Minnesota are- silver (Hypophthalmichthys 

molotrix), black (Mylopharyngodon piceus), big head (Hypophthalmichthys nobilis), and 

grass (Ctenopharyngodon idella) – are at our doorstep. These fish species have been 

raised commercially and used experimentally in aquaculture ponds in many southern 

and Midwestern states and escaped into the wild. They have since been expanding in 

the Mississippi and Illinois Rivers and their tributaries. Some of these fish feed on 

plankton at the base of the food web and their impact on invertebrates and aquatic 

ecosystems could be devastating to Minnesota’s aquatic habitats and fisheries. They 

could reach the state from either the Mississippi River and potentially through the Great 

Lakes (spread from the Illinois River). Currently, a temporary electric barrier in Illinois is 

the only protection from further invasion towards Minnesota via the Great Lakes.

However, at least one carp has been found above this barrier already. There is no 

barrier (other than existing dams) on the Mississippi to prevent upstream spread into 

Minnesota. As of 2008, no known viable populations of these fish exist in the state; 

however a grass carp was caught in the St. Croix River in the spring of 2006, a big head 

carp was caught by a commercial fisherman in the fall of 2007 on Lake Pepin, and two 

grass carp, one bighead carp, and one silver carp were caught by a commercial 

fisherman in the Mississippi River near LaCrosse, Wisconsin in November 2008 

(Associated Press).

Zebra mussels (Dreissena polymorpha) are small clams that are native to the Caspian 

Sea region of Eastern Europe. The small bivalves were introduced into the Great Lakes 

through ballast water from ships. They were first found in Minnesota in 1989 in Duluth 

Harbor of Lake Superior and have since spread to over three-dozen other waterbodies 

in the state, including the Mississippi River near Brainerd (MN invasive species 

website). It seems likely that these mussels will eventually be introduced into shallow 

lakes in the state. These mussels can be abundant and are an attractive food source 
35

for migrating and over-winter diving ducks (Petrie and Schummer 2002). In some of the 

Great Lakes, zebra mussels have attracted large numbers of diving ducks. These filterfeeding mussels also harbor environmental contaminants. The contaminants 

accumulate in the mussels’ fatty tissues. High concentrations of methyl mercury and 

polychlorinated biphenyls (PCBs) were found in mussels in Minnesota and Iowa after 

only one growing season. There is great concern that these mussels could be a source 

for translocation of contaminants into higher trophic levels of the food web including into 

waterfowl (Cope and Bartsch 1999, MacIsaac 1996). There is evidence from many 

lakes including Lake Erie that water clarity increases after introduction of zebra mussels 

due to their filter feeding. They have been intentionally introduced into lakes in the 

Netherlands as a tool to improve water clarity (MacIsaac 1996). Submerged aquatic 

vegetation could increase in lakes where these mussels become established.

Other invertebrate invasive species are cause for concern as well. Recent scuap dieoffs in Lake Winnibigoshish have been linked to the invasive faucet snail (Bithynia 

tentaculata). These small snails are native to Europe and were mostly introduced into 

the Great Lakes via ballast water. They are intermediate hosts to trematode parasites. 

Diving ducks consume the snails and are killed by the trematodes. Although faucet 

snails not been documented in any Minnesota shallow lakes yet, they may already be 

present in some and would survive if introduced, as their preferred habitats are 

freshwater ponds and shallow lakes with abundant aquatic plants (Kipp and Benson 

2008). 

Shallow lakes have been degraded by other invasive species such as hybrid cattail, 

purple loosestrife, and reed canary grass. These invasive plants have displaced 

desirable native vegetation (bulrush, wild rice, broad-leaf cattail) in some lakes and 

have altered the hydrology in many. Hybrid cattail, in particular, can clog outlet 

channels and increase sedimentation in these areas, ultimately affecting lake water 

levels. Additionally, this plant can completely in-fill all of the open water areas of lakes 

and wetlands if it is not managed. Once it has filled in a basin, it may be difficult to 

remove, especially if it forms a floating mat. Lakes completely choked by hybrid or 

narrow-leaf cattails have little value for waterfowl.

An invasive European genotype of common reed grass (Phragmites australis) has 

displaced native forms of the plant in New England states and has been found in 

isolated locations in Minnesota (Saltonstall 2002). This plant has the tendency to form 

monocultures similar to or worse than hybrid cattail. It also has the potential to alter 

hydrology and reduce open water habitats in many of the state’s shallow lakes. It could 

further displace native vegetation across the state and could be particularly threatening 

to native wild rice stands.

At least two species of submerged invasive aquatic plants, Eurasian watermilfoil 

(Myriophyllum spicatum) and curly-leaf pondweed (Potamogeton crispus) are found in 

the state and have spread to some shallow lakes. These plants can displace native 

submerged plants that are more desirable for waterfowl habitat. Curly-leaf pondweed 

can affect internal nutrient cycling resulting in mid-summer algal blooms. Once these 
36

plants are in a lake, they are nearly impossible to eliminate. Management focuses on 

reducing nuisance conditions and is expensive. Attempts at control usually involve

multiple herbicide applications, although drawdowns can be used to reduce both of 

these species. There are several other submerged invasive aquatic plants present in 

other states that would also be troublesome if introduced to Minnesota’s shallow lakes; 

hydrilla (Hydrilla verticillata) is one example.

There is evidence that climate change affects an ecosystem’s susceptibility to invasive 

species; climate change may lend to a change in species composition due to changing 

environments. Conditions may become less than ideal for native species, leaving 

systems susceptible to biological invasions. Some scientists suggest that under these 

circumstances, it may be necessary to view new species as a part of these changing 

systems rather than trying to eradicate them (Walther 2009).

Fish Rearing

Loss of wetland quantity and quality has created a scarcity of wetlands in some parts of 

the state, resulting in competition for remaining wetlands and shallow lakes. Two of 

these competing uses are fish rearing for the bait industry and for game fish stocking in 

lakes. The bait and aquaculture industry are economically and socially important in 

Minnesota. Current statutes support the use of public programs to promote aquaculture 

(M.S. 17.49) and the use of wetlands for commercial purposes (M.S. 103B.3355). Bait 

dealers can catch baitfish from wild stock in lakes and wetlands, and they can also raise 

baitfish in public waters with a permit. There is little regulation on the actual harvest of 

bait from public waters. The bait harvesters must be licensed but then can trap in 

almost any basin on which they have legal access.

The legislature has also been pressed by anglers to strongly encourage increased 

levels of walleye stocking. The fingerlings to support these stockings are raised in 

natural wetlands and shallow lake basins. More than 2,000 basins are currently 

approved for fish rearing activities; 199 of these are shallow lakes (greater than 50 

acres in size). In some shallow lakes, walleye rearing has been beneficial to reduce 

fathead minnows, improving water clarity, submerged plant abundance and aquatic 

invertebrate abundance (Herwig et al. 2004). Walleye fry predate on fathead minnow fry 

and have effectively controlled fathead minnows during the years of fry stocking. Joint 

management of wetlands has occurred successfully between DNR Fisheries and 

Wildlife and DNR Fisheries and the USFWS. Wetlands or shallow lakes are treated 

with rotenone usually by Fisheries in cooperation with Wildlife or the USFWS to remove 

bullheads and or carp and then the water bodies are used for walleye rearing activities. 

Current DNR fish rearing methods and activities do not include stocking of fatheads 

minnows or other forage fish to increase production.

Recent concerns over the impact of fish rearing has led to additional research by the 

DNR and increased interest by the state legislature. As a result, in 2006 the DNR 

unsuccessfully proposed a moratorium on the use of additional basins for fish rearing 

until ecological criteria could be established to measure the impact of rearing activities 
37

on individual wetlands and shallow lakes. The 2007 legislature required the DNR to 

submit a report on the effects of fish rearing, and this report was submitted in January of 

2008.

Physical Disturbance 

Disturbance to waterfowl by watercraft often accompanies increasing human 

populations and shoreline development. Negative impacts to waterfowl caused by 

motorized surface use of lakes has been documented both during spring and fall 

migration (Kahl 1991, Havera et al. 1992). Waterfowl often take flight when approached 

by motorboats. Boating activity related to fishing, hunting and general recreation can 

decrease the amount of time the ducks have to forage and increase energy expenditure 

through flying from the disturbance. Kahl (1991) quantified the time and energetic 

impacts of boating disturbance for canvasbacks on a Wisconsin lake. Boating 

disturbance accounted for 50% of the time canvasbacks spent away from feeding areas 

during the spring migration in this study. Several other studies have documented 

negative impacts of motor boat activities on migrating and breeding waterfowl

(Korschgen and Dalhgren 1992, Liddle and Scorgie 1980). Currently under Minnesota 

law, specific lakes can be designated Migratory Waterfowl Feeding and Resting Areas 

(MWFRAs), which restrict motorized use only during the waterfowl-hunting season. 

Recreational fisheries and high water have impacted some MWFRAs. Without 

opportunities to rest and refuel undisturbed, waterfowl move through the state quickly. 

The DNR recently completed a statewide survey of refuges and rest areas and found 

significant gaps in the statewide quantity and quality of sites available to migrating 

flocks. Although the process for establishing refuges and rest areas differs by 

ownership and type, it is usually dependent on citizen initiation and support.

In addition to direct disturbance of birds, power boating can also directly and indirectly 

impact aquatic vegetation (Asplund and Cook, 1997) and increase turbidity in shallow 

lakes (Anthony and Downing, 2003, Wagner 1991). Motors can directly impact aquatic 

plants by uprooting and cutting them. Motor boating activity particularly in shallow lakes 

with soft bottom substrates can increase phosphorus concentration in the water column

by disturbing lake sediments (Yousef et al. 1980). 

 

Increased Shoreline Development

Ever increasing demand for shoreline property has resulted in development on lakes 

that historically would not have been considered suitable for lake homes. In addition to 

increased surface use, which can lead to waterfowl disturbance, shoreline development 

usually results in loss of shoreline vegetation and submerged vegetation. Both types of 

aquatic vegetation are valuable for wildlife and waterfowl habitat. Increased 

development can result in increased pressure to manage lakes for a sport fishery, which 

can lead to further habitat changes and increased conflicts between fishermen and 

waterfowl hunters. Management based on the ecological function of a shallow lake may 

become more difficult in these situations.
38

Increased shoreline development can indirectly impact management potential of a 

basin. Drawdowns have long been recognized as valuable management tools for 

wetlands and shallow lakes, not only for waterfowl and wildlife benefits, but also for 

water quality improvements. This tool, however, is controversial and often not viewed 

as beneficial by shoreline owners. As shoreline development increases on a particular 

shallow lake, it becomes politically difficult to perform managed drawdowns on that lake. 

Climate Change

In the next 100 years, average 

temperatures in both winter and 

summer are predicted to increase 

by 5-12

o

F in winter and even more 

in the summer (Kling et al. 2003). 

Precipitation patterns are also 

predicted to change with the 

frequency of extreme weather 

events increasing by 50-100% of 

current values (Kling et al. 2003). 

The impacts of these changes on 

shallow lakes are unknown. 

However, one likely impact that may 

already be occurring is decreased 

winterkill of fish populations. Many 

studies have shown that fishless 

basins provide the best waterfowl 

habitat, but are increasingly rare (Hanson and Riggs 1995, Bouffard and Hanson 1997). 

Fishless basins tend to be small and isolated. Drainage and tiling have led to direct loss 

of these basins or connected them to other water bodies with fish. Frequent winterkill is 

one of the mechanisms that eliminate fish from a lake or wetland. Recent research 

(Fang and Stefan 2000) indicates that the likelihood of winterkill is strongly reduced in 

northern states under several predicted climate change scenarios. Ice out data from 

Minnesota also indicates a trend of shorter duration of ice cover on Minnesota Lakes 

(Figure 9). Shorter duration of ice cover would contribute to reduced frequency of 

winterkill.

There are several other potential affects of climate change that are less well understood 

including the impacts of warmer temperatures on invertebrate populations and aquatic 

vegetation. Models indicate that rainfall amounts and timing of rainfall events will be 

more variable in Minnesota. More rainfall would have negative impacts on aquatic 

vegetation in shallow lakes. The increased runoff associated with more severe rain 

events is expected to increase pollution of the state’s surface waters (Carstensen et al. 

2008). This added pollution would also have negative impacts on aquatic vegetation 

and waterfowl habitat. Increased warming may lead to increased summer water 

temperatures could exacerbate internal phosphorus loading in lakes (Malmaeus et al. 

Figure 9. Average date of lake ice out from historical data 

on several lakes across the state. Pink dashed line 

represents short term trends.
39

2006). Management strategies to deal with or reduce internal nutrient loading will 

continue to be needed.

OPPORTUNITIES AND MANAGEMENT APPROACHES

The multiple problems affecting shallow lakes require a variety of tools to address those 

problems. Some of the most common tools are summarized below. While this and 

other plans will provide the overall framework for a state-wide management approach, 

each managed lake will require an individual management plan that will include multiple 

strategies and tools to deal with specific impacts or threats. Shallow lake management 

requires ingenuity and creativity; therefore this list is not comprehensive, and new tools 

may be developed. The tools in this summary can be divided into three basic 

categories: direct protection, habitat and water quality improvement, and regulatory and 

policy protections.

Direct Protection

Some shallow lakes in the state are in good condition both with respect to waterfowl 

habitat and water quality. The primary management objective for those lakes should be 

to maintain and protect that existing habitat. The likely reason some of these lakes 

remain in good condition is absence of invasive species, small watershed with less 

development or little loss of native vegetation and wetlands, and lack of extensive 

shoreline development. For such lakes surface use restrictions could be implemented 

to protect the aquatic plants, maintain water clarity, and minimize disturbance. 

Watershed and shoreline protection can be done through direct acquisition from willing 

sellers and through conservation easements available through various programs and 

non-profit organizations (RIM, WRP, USFWS, NRCS, SWCDs and DU). Additionally,

new programs providing incentives for conservation easements or acquisitions targeted 

for shallow lake watersheds and lakeshores could be developed. All of the above tools 

require working cooperatively with various partners. 

Criteria to consider for targeting lakes for direct protection are: quality of existing habitat, 

size of watershed (smaller the better), waterfowl use, water level management potential, 

and proximity to features that would contribute to a complex of habitat.

Such tools can also be applied to degraded lake systems as a part of a comprehensive 

habitat restoration plan that includes in-lake management. Research on shallow lake 

management demonstrates that watershed restoration is not sufficient to restore water 

clarity and plants in degraded shallow lakes due to continued internal nutrient loading.

However, wetland and grassland restoration and protection would also serve additional 

benefits by forming habitat complexes of shallow lakes, wetlands and grasslands. 

These complexes are a key component of achieving the goals of the Duck Plan.
40

Habitat and Water Quality Improvement Tools

Shallow prairie lake ecosystems evolved under climatic conditions that featured periodic 

droughts of varying degrees of intensity. Severe droughts typically occurred every 8-15 

years with mild droughts occurring about twice as often. The result was basins with 

good quantities of emergent vegetation such as bulrush and lush submerged 

vegetation. The periodic droughts combined with severe winters to limit fish populations. 

Lakes with flowing outlets often harbored game fish that moved upstream in the spring. 

The surrounding uplands were typically dense prairie grass that enhanced infiltration of 

rain, minimizing the amount of run-off into lakes and streams. Changes mentioned 

above (climate change, altered hydrology) have reduced or eliminated natural drought 

cycles.

Drawdown

The most effective management technique mimics historical droughts through water 

level manipulation known as a “drawdown”. A drawdown is an effective and relatively 

inexpensive shallow lake management tool that addresses both problems with internal 

nutrient loading and loss of aquatic plants. This temporary water level manipulation 

restores aquatic vegetation, improves water clarity, removes fish or temporarily reduces 

fish abundance and increases invertebrate abundance. Sediments are consolidated 

when they are subjected to drying, reducing wave re-suspension thereby increasing 

water clarity when the basin is re-flooded. Sediments are also aerated, reducing 

release of phosphorus into the water column. Additionally, many aquatic plant seeds, 

especially bulrush, need to be dried or need mud flats to germinate. Since natural 

droughts occur periodically, drawdowns will also need to be repeated over time as 

habitat conditions change. 

Fish Management

On many basins, drawdowns are not possible. Some lakes do not have outlets, or the 

outlets lack sufficient change in topography to lower water levels. Lakes with large 

watersheds are difficult to drawdown. For these basins, other tools need to be 

considered including rotenone treatments, fish barriers and predator fish stocking. 

These tools need to be applied to appropriately identified problems in conjunction with 

individual lake management plans. Like drawdowns, fish management in shallow lakes 

is an on-going process; the results of any single treatment are not going to last 

indefinitely. Management and treatments will need to be repeated if habitat quality is to 

be maintained. 

Fish barriers are installed to prevent or reduce carp populations. Barriers come in 

several different types and configurations including physical barriers, mechanical 

barriers and electric barriers. These barriers reduce or prevent upstream movement of 

fish. Preventing downstream movement is more difficult. The site and budget will 

determine which barrier is best suited to a particular site. Ideally, these barriers are 

placed prior to drawdowns or chemical treatments aimed at reducing fish populations. 
41

Basins that have limited connections to other water bodies are the best candidates for 

fish barriers. In many situations however, it is difficult to find an effective fish barrier or 

means of removing fish above a barrier.

Rotenone is a piscicide derived from plants from the Derris genus. It has been used as 

a fisheries management tool for decades. Wildlife managers in Minnesota and 

elsewhere use this chemical primarily to manage carp in shallow lakes. Due to the cost 

and overall desire to limit chemical treatments, this tool is usually used when full 

drawdowns are not possible as a means of fish control. Rotenone can be most effective 

when applied to isolated water bodies, those either naturally isolated or through means 

of fish barriers. However due to the difficulty of obtaining effective treatments in 

shallow, nutrient rich systems, treatments may need to be repeated or combined with 

drawdown. It typically is applied in the late fall, but a specific treatment plan needs to be 

prepared for each basin considered for such a treatment.

Predator fish stocking has been studied as a management tool for degraded systems, 

including wetland systems in Minnesota. The idea is predators can control lower trophic 

levels and ultimately result in reduced algal biomass. An example of predator stocking 

in Minnesota has involved experimental stocking of walleye to control fathead minnows 

in wetland systems (Herwig et al. 2004). In the simplest explanation, walleye fry eat 

fathead fry, zooplankton populations are able to increase and these zooplankton reduce 

algae abundance through their filter feeding activities. Northern pike have been used in 

other states to try to reduce carp recruitment (Cunningham, personal communication). 

Carp reach a large enough size in their second year of growth to escape predation 

pressure by other fish; however control likely occurs at larval or early stages. Research 

has also shown that this tool is usually not effective when used alone but should be 

combined with other management treatments (Scheffer 2004).

Fish populations can naturally occur in shallow lakes. Historically, they have been 

periodically limited by winter-kill, although less so more recently as discussed earlier. 

Popular game species including northern pike, largemouth bass, sunfish, perch and 

crappies can all naturally occur in some shallow lakes. Given the natural occurrence of 

these species, it may be appropriate to use fish as a management tool in these shallow 

lakes. In fact, it will be necessary in many lakes to manage them in part for recreational 

fishing opportunities. In many shallow lakes, it is not feasible to manage them without 

fish. Game fish may provide some competition and control, as mentioned above, of less 

desirable species. Conflicts between waterfowl hunters and fishermen have occurred 

when management of fish and waterfowl interests do not align. Fish populations can be 

maintained by aeration even when water quality and aquatic plant abundance has 

deteriorated, resulting in lakes with recreational fishing opportunity but poor water 

quality and wildlife habitat. When fish are present or used as a management tool in 

shallow lakes, careful balance of expectations both among resource managers and the 

public are necessary. When aeration is considered to maintain gamefish populations, 

ultimate goals should be to maintain good water quality. In “deeper” shallow lakes, or 

tweeners, aeration may be used as a tool to maintain piscivorus fish aimed at controlling 

carp and other fish that contribute to internal nutrient loading. Everyone will need an 
42

appreciation of the dynamic nature of these systems for such management approaches 

to be successful.

The general public often perceives some of these in-lake tools, including drawdowns 

and rotenone treatments, as being overly drastic. Research on management of 

degraded shallow lakes indicates that these drastic measures are exactly what is 

needed to overcome multiple stressors (loss of plants, abundant algae, suspended 

sediments, internal nutrient loading from fish) that are maintaining the poor habitat and 

water quality conditions.

These in-lake strategies should be combined with watershed restoration and protection. 

Key watershed tools are best agricultural management practices and wetland and 

grassland protection and restoration. Biomanipulation attempts are more likely to be 

successful in improving water clarity in those cases where watersheds have more 

grassland (Reed 2006).

Restoration and protection of watersheds could also make these shallow lakes more 

resistant and resilient to impacts caused by many different stressors including climate 

change. Loss of biodiversity and function makes systems less resistant to impacts 

including pollution and climate change (Folke et al 2004). The resilience of ecosystems 

can be reduced by anthropogenic pressures and ultimately affect ecosystem function. 

An ecosystem’s capacity to absorb changes and “repair” itself is not a certainty, thus 

adaptive management will be necessary to maintain ecosystem function or desired 

ecological states (Folke et al. 2004).

Habitat Management for Wild Rice

Management of lakes for wild rice has been focused in the forested part of the state. 

Historically, the native range of this plant extended well beyond the forested regions of 

the state, but it is not currently common in lakes much beyond the transitional zone. 

Lakes in the forested region have been less impacted by wetland drainage. 

Management for wild rice has included removal of beaver dams or cattail bogs that have 

obstructed lake outlets. This management is relatively inexpensive, yet effective. 

Removing outlet obstructions minimizes both high water and rapid water level changes, 

which can damage wild rice.

In some instances, water levels on historic wild rice lakes have been raised or stabilized 

by installation of dams, or the outlets were impacted by road culverts. Simply modifying 

the dam or outlet structure to allow historical water levels and natural fluctuations can 

be enough to restore wild rice. Lake Onamia is an example of wild rice restoration by 

outlet dam replacement. 

There are some lakes that historically have produced wild rice, but it is unlikely a viable 

seed bank remains due to the number of years since it has grown. Seeding may be 

considered if the reason for the original loss of wild rice has been mitigated.
43

Regulatory Tools for Protection of Shallow Lakes and Wildlife Resources

Legal Issues Associated with Water Level Management and Lake 

Designation Through M.S. 97A.101

Water levels and water management is governed through M.S. 103G and associated 

rules in Chapter 6115. Changes in water levels or active management of water levels in 

lakes is difficult to achieve in many cases due to requirements in statute. There are 

some allowances in statutes that can allow water level management through permitting 

and following of statutory procedure/requirements. A limitation of the 103G statute is the 

regulatory authority is below a lakes Ordinary High Water (OHW) Level only. It does not 

regulate some practices around lakes that can ultimately impact lake water levels and 

water quality. For example, a field can be tiled and out-letted into a protected water 

body as long as the tile outlet is above the OHW level. Mitigation of such water level 

impacts involves work below the OHW level, thus requiring sometimes multiple permits 

and regulatory approvals so at times it seems that the scales are tipped against wildlife 

managers desiring to protect and improve habitat and water quality in shallow lakes.

Management of water levels in lakes and wetlands can be governed by many laws and 

levels of government which makes implementing new water level management projects 

a complicated and lengthy process. Such management is regulated by the state both 

through DNR and the Board of Water and Soil Resources through M.S. 103A-G statutes 

(and the Wetland Conservation Act M.R. Chapter 8420). The Army Core of Engineers 

also has regulatory authority over some of these projects. Any water management 

project involves coordination with multiple entities and agencies that may have 

regulartory authority over a particular aspect of a project, resulting in a long and usually 

complicated process toward implementation.

M.S. 97A.101 is one of the strongest legal management tools available to the Section of 

Wildlife for shallow lake management purposes. This authority was originally passed by 

the legislature in1969 by adding language to Section 97.48 subdivision 11 of the 1967 

Session Laws. This additional authority to manage water levels for the benefit of wildlife 

was added due to the support from the Southern Minnesota Waterfowl Association and 

other sportsmen’s groups. The new statutory language gave the department the

authority to manage water levels on designated lakes for the benefit of wildlife without 

obtaining written permission or flowage easements from all riparian landowners. Legal 

requirements include legal notice and a public hearing on the proposed management.

Originally the statute applied to the portion of the state south of U.S. Highway 12. In 

1975, the statute was modified to apply to the entire state. Further modifications have 

occurred to the statute including the prohibition of airboat use on designated lakes and 

the addition of authority to restrict motorized surface use. 

Other legal mechanisms to manage water levels in lakes are also available and include: 

obtaining flowage easements from all riparian landowners, acquiring all shorelines 
44

through fee-title purchase or obtaining signatory permission for one-time drawdowns. 

Wildlife Lake Designation is the most public of these options as an extensive review 

process is required. Through this statute, drawdowns can be conducted without 

permission from all landowners, making it the only viable option for water level 

management authority in some cases. One-time signatures are not often used to gain 

management permission, as a capital investment in a water control structure would not 

be made without long-term management authority. In 2009, additional language was 

passed (M.S. 103G.408) by the legislature allowing drawdowns if 75% of riparian 

owners signed off on the proposed management and a public hearing was held. This 

new language may offer expanded water level management opportunities beyond those 

for wildlife benefits. Further changes in statutes that regulate drainage surrounding 

lakes and water level management may be needed to fully achieve goals of this plan or 

to deal with problems of water quality in lakes beyond the scope of this plan.

The lake designation process is long and can be controversial. Survey and feasibility 

studies are often needed to determine management potential. Legal access and control 

of the lake outlets are required in order to construct structures. Landowners and local 

units of government are involved in the process and review of draft management plans. 

As of February 2010, 44 lakes have been designated for wildlife management purposes.

Shoreline Classification

Shallow lakes have few regulations and statutes that apply specifically to wildlife and 

waterfowl habitat. These lakes receive protection under shoreline rules, as do all public 

waters. Many shallow lakes fall under the zoning classification of Natural Environment 

Lakes, which have the most stringent shoreline development standards of the current 

classifications. Statewide shoreline management standards may soon undergo revision 

with options to increase protections of sensitive shorelines/areas, many of which would 

likely be on shallow lakes. Current standards allow local units of government to 

implement more stringent standards than the basic statewide standards. Some 

counties have implemented special standards on lakes with sensitive habitats including 

some shallow lakes. Current Aquatic Plant Management Rules also limit aquatic 

vegetation removal on all protected water bodies.

Surface Use and Hunting Regulation

There are options to limit surface use of shallow lakes in order to reduce disturbance to 

waterfowl and/or protect aquatic vegetation from damaged caused directly by 

motorboats or indirectly from increased turbidity caused by motor-boating activities. 

Wildlife lake designation statute including Minnesota Statute 97A.101 provides the 

authority to restrict motorized surface use on Designated Wildlife Lakes. This is the 

only tool available for limiting motor-boating activity outside of the waterfowl-hunting 

season for the benefit of waterfowl.
45

The intent of the following regulations is to protect migrating waterfowl. These 

regulations apply only during the waterfowl-hunting season and do not protect the lake 

habitats that waterfowl are using. 

MWFRAs can be used to minimize boating disturbance but only during the waterfowl 

season. MWFRAs are open to hunting, but not motorized boat use (M.S. 97A.095) 

Refuges can be used to limit hunting-related disturbance during the waterfowl-hunting 

season. Lakes within refuges are closed to hunting but not other forms of surface use. 

Surface use is not restricted during the rest of the year. (M.S. 97A.085 and 97A.095).

Migratory Waterfowl Sanctuaries can be used to prevent all surface use, including 

hunting, during the waterfowl-hunting season. Lakes within Sanctuaries are open to 

surface use the rest of the year. (M.S. 97A.095).
46

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Appendix A: Distribution Maps of Shallow Lakes Targeted for Management
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