Lake protection and management

Every lake is unique. Long-term management considers the environmental, cultural, and biological factors affecting the lake and sets a priority on finding lasting solutions.

Lake management is complicated and requires a coordinated effort of community groups, individuals, landowners, and government. To be effective, lake managers must commit to long-term strategies and investment. Specific strategies to address a lake's nutrient enrichment problems must focus on activities in the watershed and, if needed, in-lake restoration techniques.

Guide to Lake Protection and ManagementThe second edition of the Citizen's Guide to Lake Protection (2004) contains updated and new material on the following topics: chemistry of lakes, watershed information, exotic species, altering runoff and lake use practices, development of a lake management plan, and nonstructural best management practices.

PDF icon Guide to Lake Protection and Management, Second Edition

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A lake is an ecosystem, a biological community of interaction among animals, plants, and microorganisms as well as the physical and chemical environment in which they live. Water bodies are generally considered to be lakes when they are at least ten acres in surface area and greater than six feet deep at some point.

Lakes are interconnected with other water resources, and receive much of their water from streams and groundwater. Wetlands adjacent to the lakes, or connected to lakes by streams, often serve as spawning grounds for fish and habitat for diverse species of plants and animals. Protection of all of these natural resources as a whole is vital to the protection of lakes.

A complex interdependence has evolved among the organisms in a lake community. If one part of the ecosystem is disturbed, it affects other parts. Well-balanced lake ecosystems, however, do change from season to season and from year to year. Short-term events, such as an unusual or excessive algal bloom, may not necessarily signal a long-term problem.

On the other hand, changes in land use in the watershed may not immediately have a visible effect on the lake. For example, it may take a decade or more for changes in agricultural practices or urbanization to result in weed problems or fish kills.

A necessary prerequisite for deciding how to protect a lake is developing a basic understanding of the physical, biological and chemical properties of a lake.

The physical

Stratification: Lakes form layers

lakelayers Lakes in the temperature climates tend to form layers. The epilimnion is roughly equivalent to the zone of light penetration where the bulk of productivity, or growth, occurs. The thermocline is a narrow band of transition which helps to prevent mixing between the layers. The hypolimnion is the zone of decomposition, where plant material either decays or sinks to the bottom and accumulates.

Lakes in temperate climates tend to stratify or form layers, especially during summer, because the density of water changes as its temperature changes. Water is most dense at 39°F. Both above and below that temperature, water expands and becomes less dense. This means that in the spring, just before the ice melts, the water near the lake bottom will be at 39°F. Water above the lake bottom will be cooler, approaching 32°F just under the ice.

As the weather warms, the ice melts and the surface waters begin to heat up. Wind action and increasing water density causes this surface water to sink and mix with the deeper water, a process called spring turnover.

As summer progresses, the temperature and density difference between the upper and lower lake water becomes more distinct, and most deep lakes form three separate layers. The upper layer, the epilimnion, is characterized by warmer water. The epilimnion is roughly equivalent to the zone of light penetration, where the bulk of productivity, or growth, occurs. Much of the plant and fish life is found in this zone.

Below the epilimnion is another layer, the thermocline, in which the temperature declines rapidly. The thermocline is a narrow transitional band between the warmer, upper and lower, cooler layers that helps to prevent mixing between the layers.

Below the thermocline lies water much colder than the epilimnion, called the hypolimnion. The hypolimnion is the zone of decomposition, where plant material either decays or sinks to the bottom and accumulates. Dissolved oxygen levels are often very low in this layer.

These temperature conditions will continue until fall. Then surface waters cool until they are as dense as the bottom waters and wind action mixes the lake. This is the fall turnover.

The biological

A lake can be divided into zones, or communities, of plants and animals. Extending from the shoreline is the littoral community, where aquatic plants are dominant. The size of this community depends on the extent of shallow areas around the lake and the clarity of the water for light penetration. Water lilies, duckweed, and submerged plants are abundant. These plants play an important role in the overall aquatic community by producing oxygen and providing food and shelter for insects, crustaceans, frogs, turtles, and fish. Maintaining the health and integrity of this zone is critical to the overall health of the lake.

The area of open water is the limnetic community. This area is the habitat of phytoplankton (algae), zooplankton (microscopic animals) and fish. Phytoplankton are very important, serving as the base of the lake’s food chain and producing oxygen. The process by which green plants, including algae, produce oxygen from sunlight, water, and carbon dioxide is photosynthesis. Chlorophyll is a pigment produced by the plants, which is essential for this process. Since sunlight is very important for photosynthesis, oxygen will be produced only as deep as the sunlight penetrates. The depth of light penetration can be measured using a Secchi disk.

Below the limnetic zone is the profundal community, where light does not penetrate. This zone or community is dominated by respiration, or oxygen consumption, rather than oxygen production. This zone corresponds roughly to the hypolimnion layer. The community in this zone consists of such organisms as bacteria and fungi. These organisms decompose dead plants and animals that descend from the waters above. This process consumes oxygen.

The chemical

Plants require various substances for growth, including phosphorus, carbon, oxygen, and nitrogen. The concentrations of these substances in water control the total amount of plant matter that can grow. The quantity of each required substance varies.

For example, a high percentage of all plant matter is carbon and a very small percentage is phosphorus. If any one of these substances is absent, plants cannot grow, even if the other substances are abundantly available. In many lakes, phosphorus is the least available nutrient; therefore, its quantity controls the extent of algal growth. If more phosphorus is added to the lake from sewage treatment plants, urban or farmland runoff, septic tanks, or even from phosphorus-rich sediments stirred up from the lake bottom, more algae will grow.

In turn, the amount of algae in the water will determine how deep light penetrates as measured by the Secchi disk. Combined measurements of phosphorus level, algae abundance (expressed in terms of chlorophyll a) and Secchi disk transparency are used to identify the trophic status or the level of growth of a lake. A eutrophic or nutrient-rich lake tends to be shallow, “green,” and has limited oxygen in the hypolimnion. An oligotrophic lake is relatively nutrient-poor, is clear and deep, and has a hypolimnion high in dissolved oxygen. A mesotrophic lake is intermediate between the two. Factors vary, however, from lake to lake, and assessments are necessarily subjective.

Other chemical factors also play an important role in lake ecology. The acidity of water, measured by the pH scale, is an important consideration for aquatic life. A desirable range in pH for aquatic life is 6.5 to 9.0. Values either higher or lower may interfere with reproduction, respiration and other biological functions of aquatic life. Alkalinity, or buffering capacity, determines the ability of water to withstand great fluctuations in pH. The alkalinity of a lake generally depends on minerals, such as lime, in its watershed. Watersheds with soils rich in lime and related materials will provide much buffering to lakes, while those poor in lime, such as the bedrock region of northeastern Minnesota, will provide very little buffering capacity to lakes. These poorly buffered lakes are more susceptible to changes in pH and acid deposition or acid runoff.


Eutrophication is the process by which lakes are fertilized with nutrients, which are chemicals absorbed by plants and used for growth. It is a natural aging process, but human activities can speed it up – with more algae and aquatic plants, often called weeds, the result.

As nutrients such as nitrogen, phosphorus, and potassium, wash into lakes in runoff water or by soil erosion, these chemicals fertilize the lake, allowing algae and weeds to grow. As plants die and decompose, they accumulate on the lake bottom as muck. After hundreds or thousands of years of plant growth and decomposition, the character of a lake may more closely resemble a wetland. This process is natural, but various human activities can literally make a lake “old” before its time.

Nutrients washed from agricultural areas, stormwater runoff from urban areas, municipal and industrial wastewater, runoff from construction projects, and even recreational activities contribute to cultural eutrophication. When human activities increase the rate of nutrient and sediment enrichment of a lake, pollution is occurring.

Nutrient and other pollution sources discharged to a lake from specific locations, such as municipal and industrial wastewater outlets, urban stormwater outlets, or other “point” sources are easy to identify. This type of pollution is also relatively easy to control through treatment projects and has been the focus of much of the water pollution control work to date.

Nutrients and pollution sources that are not discharged from a specific pipe, but instead are washed off the land or seep into groundwater, are known as nonpoint sources of pollution or polluted runoff. These include runoff from agricultural fields and feedlots, leakage from septic tanks, nutrients from wetland drainage and stormwater runoff, and others. Polluted runoff is best controlled through wise land use practices, also known as best management practices (BMP’s).


Closely associated with eutrophication is sedimentation. Wind and water move soils from the surrounding watershed into a lake, a process known as erosion. These soils settle on the bottom of the lake causing the lake to become increasingly shallow. This process is a natural part of lake aging, governed by gravity and the forces of rain and wind.

Erosion and sedimentation can be greatly accelerated by human activities that leave the soil without vegetation for extended periods. Construction activities that cause soils to be bare and intensive agricultural activities, such as plowing near lakes and streams or farming steep slopes, leave soils vulnerable to erosion. This problem is best controlled through soil and water conservation practices and maintaining vegetation on soils.


Acid rain occurs when air pollution, sulfur and nitrogen oxides from power plants, factories and cars mix with cloud moisture to form acidic compound which eventually fall to earth in rain, snow or dust. Acid rain can change the chemical balance of a lake, sometimes with severe consequences.

In Minnesota, lakes in the northeastern part of the state are considered the most sensitive to acid rain because of their very low alkalinity. The concern raised about acid rain in the 1980s lead to the creation of state and federal emission control laws that reduced emissions and virtually eliminated the potential for acidification of Minnesota’s lakes.

Another reason that Minnesota lakes never were acidified is that natural bacteria convert the sulfate from sulfuric acid to hydrogen sulfide, a process that consumes the acid. Unfortunately, new research has shown that these same bacteria produce methylate mercury. Methylmercury is the only form of mercury that accumulates in fish. Therefore, it is probable that acid rain has contributed to increased mercury contamination of fish, even in the absence of acidification. As a result of the state’s glacial history, much of northeastern Minnesota and parts of north central Minnesota have thin soils and exposed bedrock.

Most of the state’s acid-sensitive lakes are in these areas. Moreover, these areas receive an average rainfall of pH 4.6, ten times more acidic than normal rain (pH 5.6). In contrast, agricultural lands in southern and western Minnesota receive rain with a close-to-normal pH and also have a low sensitivity to acid rain.

Toxic contamination

Toxic chemicals may enter and contaminate lakes from a variety of sources:

  • industries use chemicals that may enter lakes from direct discharge or runoff from their facility;
  • farmers use pesticides or herbicides that may runoff into lakes;
  • urban storm runoff containing metals, salts and pesticides may enter lakes;
  • wastewater discharge may contain pharmaceuticals that can enter lakes; and,
  • chemicals in the air, in particular mercury, may enter lakes in rain and snow.

Toxic contamination may be dramatic — such as fish kills that eliminate part or all of a lake’s fish population. Less obvious impacts may include decreased reproduction or slower growth rates in fish and other aquatic life.

One particularly dangerous impact is the bioaccumulation or build-up of toxic substances in fish at the top of the food chain. The most widespread example of this concern is mercury contamination of piscivorous fish, which occurs in virtually every lake because of air pollution. Not only may these fish experience effects on their ability to reproduce, but the toxic effects may be passed on to humans and wildlife eating the fish.

Because of potential health effects, Minnesota has fish consumption advisories for mercury on virtually every lake in the state and for PCBs (polychlorinated biphenyls) on a few lakes. Fortunately, PCBs are no longer manufactured, therefore the concentration of PCBs in Minnesota fish has declined markedly during the past decade. There is some evidence that efforts to reduce mercury use and emissions are also resulting in fish with lower levels of contaminants.

Exotic species infestation

Another threat to lakes is the infestation of the lake by exotic species. Several exotic species have caused considerable harm to our lake ecosystems. Because these species are imported from another area or country, they do not have natural predators. This allows them to grow and out-compete many of our native species.

Scientists are working to develop methods to control these exotic species. The best control is preventing introduction of the plant or animal species to a lake. Educational efforts to teach the public about preventing introduction of these species are ongoing. Learn to recognize these species. Some of the exotics found in Midwestern lakes include Rusty Crayfish, Zebra Mussels and Curlyleaf Pondweed, to name just a few.


Lake management

First, we need to understand that what we do on land and in the water affects the lake. We need to consider the intricate lake ecosystem and the interdependence between the lake and its surrounding watershed. We need to recognize that lakes are vulnerable, and that in order to make them thrive, citizens, both individually and collectively, must assume responsibility for their care.

Lake management is a process. A lake manager displays a willingness to study a lake, to assess its status and its needs and to determine how best to maximize the lake’s potential as a thriving ecosystem. Lake management can be as simple as fostering the practices of stewardship among lake homeowners and other interested individuals. It can also include taking an active role in altering specific ecological relationships within the lake and its watershed to

Lake restoration

Lake restoration is an action directed toward a lake to “make it better.” It is one example of a lake management technique. The complexity and expense of this activity requires an organization with some authority over the lake and its watershed, such as a lake improvement district or watershed district. It can also be accomplished through a cooperative effort of many groups, such as the lake association, city, watershed organization, or state agency.

Lake restoration is sometimes associated with chemical treatment of a lake. Usually, lake restoration is much more than this. Treating the lake with chemicals is like putting a bandage on the injury; it does not stop the harming event from happening again and will only be temporarily effective in masking the problem.

Because it may take years for external source controls to result in improved lake water quality, in-lake restoration techniques have been developed to accelerate recovery. These techniques may not be suitable for all lakes and all conditions. Consider using these techniques only after a lake specialist has evaluated the lake and recommended one or more of these options.

Listed below are overviews of some common in-lake techniques. Please refer to the third edition of Restoration and Management of Lakes and Reservoirs, authored by G. Dennis Cooke, Eugene B. Welch, Spencer A. Peterson, and Stanley A. Nichols, 2005, for a comprehensive and scientific discussion of these and other lake management methods.

Check with state and local agencies to determine which permits are required before proceeding with any of these activities. MPCA issues permits for continuous in-lake treatment systems, which collect and treat inflow to a lake. Contact the MPCA for more information about this process.

Hypolimnetic aeration. Oxygen is pumped into the deep, nutrient-rich layer that forms in deep lakes in order to maintain oxygen to limit phosphorus release from sediments without causing the water layers to mix (destratify).

Hypolimnetic withdrawal. Siphons are used to remove nutrient rich water from the hypolimnium, reducing nutrients and eliminating some of the low oxygen water. Hypolimnetic withdrawal is suitable for small, deep lakes but can have severe repercussions on downstream receiving waters which receive nutrient-enriched waters.

Artificial circulation (aeration). Artificial circulation provides increased aeration and oxygen to a lake by circulating the water to expose more of it to the atmosphere and is generally used in shallow water bodies. This can include surface spray (fountains), paddlewheels, and air diffusers.

Nutrient diversion. Drainage channels or pipes are used to divert nutrient-rich waters to the downstream side of lakes. This could include the diversion of existing industrial or domestic wastewater from this lake.

Dredging. Heavy equipment or specialized hydraulic dredges can remove accumulated lake sediments to increase depth and eliminate nutrient-rich sediments, controlling rooted aquatic vegetation, deepening the water body, and increasing lake volume.

In-lake treatment or nutrient inactivation. Aluminum, iron, or calcium salts can inactivate phosphorus in lake sediments. Phosphorus generally limits the growth of freshwater algae in most Minnesota lakes, although nitrogen is also an important nutrient.


External sources such as fertilizer use, pet wastes, stormwater runoff, septic system effluents, waterfowl, agriculture and even rainfall can contribute nutrients to a lake. Lake management removes or modifies as many of these nutrient sources as possible, especially those sources shown to be contributing the greatest nutrient load to the water body.

Long-term management of excessive algae requires the removal of phosphorus sources to the water body, which in effect reduces the algae in the lake. If in-lake restoration techniques are necessary, they should be proceeded by or occur alongside appropriate long-term management actions to control sediments, nutrients, and toxic inputs. A successful lake restoration program should strive to manage both external and internal nutrient sources.

What is in-lake treatment?

Phosphorus enters the water either externally, from run-off or groundwater, or internally, from the nutrient rich sediments on the bottom of the lake. Phosphorus is released from the sediments under anoxic conditions that occur when the lake stratifies and oxygen is depleted from the lower layer. Even when external sources of phosphorus have been curtailed by best management practices, the internal recycling of phosphorus can continue to support explosive algal growth. In-lake treatments are used to control this internal recycling of phosphorus from the sediments of the lake bottom.

How does it work?

Lake projects typically use aluminum sulfate (alum) to inactivate phosphorus. When applied to water, alum forms a fluffy aluminum hydroxide precipitate called a floc. As the floc settles, it removes phosphorus and particulates (including algae) from the water column (precipitation). The floc settles on the sediment where it forms a layer that acts as barrier to phosphorus.

Phosphorus, released from the sediments, combines with the alum and is not released into the water to fuel algae blooms (inactivation). Algal levels decline after alum treatment because phosphorus levels in the water are reduced. The length of treatment effectiveness varies with the amount of alum applied and the depth of the lake. Alum may also be applied continuously by injecting small doses into water flowing into the lake to precipitate phosphorus from the water column (see below for information on permitting of these systems).

ALUM (aluminum sulfate). On contact with lake water, alum forms a fluffy aluminum hydroxide precipitate called floc. Aluminum hydroxide (the principle ingredient in common antacids such as Maalox) binds with phosphorus to form an aluminum phosphate compound. This compound is insoluble in water under most conditions so the phosphorus can no longer be used as food by algal organisms. As the floc slowly settles, some phosphorus is removed from the water. The floc also tends to collect suspended particles in the water and carry them down to the bottom, leaving the lake noticeably clearer. On the bottom of the lake the floc forms a layer that acts as a phosphorus barrier by combining with phosphorus as it is released from the sediments.

IRON. Phosphorus forms precipitates and complexes with iron. In oxygenated, alkaline conditions (common in the entire water column during spring and fall mixing), iron is oxidized to the ferric form. Fe(OH)3 absorbs phosphorus from the water column and forms a barrier over the sediment surface, providing high sediment phosphorus retention, greatest at pH 5-7. FePO4 also forms, but the primary means of phosphorus removal and retention in sediments is sorption to Fe(OH)3. During summer and winter, deep lake water is dark and isolated from mixing. Without net photosynthesis or aeration by mixing, pH and dissolved oxygen concentrations decline in the water overlying the sediments. In low dissolved oxygen, iron is used by the microbial community as an alternative electron acceptor to oxygen and phosphorus is released. Iron’s reaction to low oxygen and pH conditions means that aeration or artificial circulation may have to accompany application to prevent the breakdown of the oxidized barrier or a photosynthetically caused increase in pH.

Why treat a lake?

Increased nutrient loading (particularly phosphorus) has accelerated eutrophication of lakes and consequently reduced their ecological health and recreational value. Frequent and pervasive algal blooms, low water transparency, noxious odors, depletion of dissolved oxygen, and fish kills frequently accompany cultural eutrophication. External sources of phosphorus delivered in run-off from the watershed are often the main contributor of excessive phosphorus to lakes.

Typically, the first steps taken in a lake rehabilitation effort target control of external sources of phosphorus and can include:

  • encouraging the use of phosphorus free fertilizers,
  • improving agricultural practices,
  • reducing urban run-off, and
  • restoring vegetation buffers around waterways.

Lake researchers have learned that lakes are very slow to recover after excessive phosphorus inputs have been eliminated. This is due to the fact that lake sediments become phosphorus rich and can deliver excessive amounts of phosphorus to the overlying water. When dissolved oxygen levels decrease in the bottom waters of the lake (anaerobic conditions), large amounts of phosphorus trapped in the bottom sediments are released into the overlying water. This process is often called internalnutrient loading.

The length of treatment effectiveness varies. A number of case studies have been conducted on lakes that have undergone nutrient inactivation with alum. Eugene Welch and Dennis Cooke (1995) evaluated the effectiveness and longevity of treatments on 21 lakes across the United States. They concluded that the treatments were effective in six of the nine shallow lakes, controlling phosphorus for at least eight years on average. Applications in stratified lakes were highly effective and long lasting. Percent reduction in controlling internal phosphorus loading has been continuously above 80 percent. The study did however find that alum treatment of lakes with high external loading was not effective.

Is chemical treatment toxic to aquatic life?

Some studies have been conducted to determine the toxicity of aluminum for aquatic biota. Freeman and Everhart (1971) used constant flow bioassays to determine that concentrations of dissolved aluminum below 52 ug Al/L had no obvious effect on rainbow trout. Similar results have been observed for salmon. Cooke, et al (1978) adopted 50 mg Al/L as a safe upper limit for post-treatment dissolved aluminum concentrations. Kennedy and Cooke (1982) indicate that based on solubility, dissolved aluminum concentrations, regardless of dose, would remain below 50 ug Al/L in the pH range 5.5 to 9.0.

A dose producing post-treatment pH in this range could also be considered environmentally safe with respect to aluminum toxicity. MPCA guidelines for alum application require that the pH remain within the 6.0-9.0 range. According to Cooke et al (1993) the most detailed study of the impact of alum treatments on benthic insects was that of Narf (1990). He assessed the long term impacts on two soft water and three hardwater Wisconsin lakes. He found that benthic insect populations either increased in diversity or remained at the same diversity after treatment.

The treatment of lakes with alkalinities above 75 mg/L as CaCO3 are not expected to have chronic or acute effects to biota. Fish related problems associated with alum treatments have been primarily documented in soft water lakes. However, many softwater lakes have been successfully treated with alum, when the treatments are pH buffered.

Are there health concerns for people?

Concerns about a connection between aluminum and Alzheimer’s have been debated for some time. More recent research points to a gene rather than aluminum as the cause. In addition, aluminum is found naturally in the environment. Some foods are high in aluminum, including tea, spinach and other leafy green vegetables. Use of aluminum cookware has not been found to contaminate food sources.

How much does an alum treatment cost?

Costs of alum application are primarily dependent on the form of alum used (wet or dry), dosage rate, area treated, equipment rental or purchase and labor. The cost is dependent on dosage requirements and costs to mobilize equipment. Treatment costs range from $280/acre to $700/acre. Liquid alum has been used when large alum doses were needed, and averages $1.75 per gallon.

How does the MPCA regulate in-lake treatment?

When MPCA receives a request for in-lake treatment, MPCA Standards and Watershed staff work together to address external load reductions that are either occurring or planned. The MPCA works with Department of Natural Resources (DNR) Fisheries staff to discuss impacts to aquatic plants and fish.

Many of the known chemicals, applied in a watershed with robust external load reductions, can be approved more quickly than lesser known chemicals in watershed that have not identified external loading opportunities. If approved, the proposer will be sent a letter with guidelines from MPCA on notifications to local partners (DNR), monitoring during and after the event, and the acceptable pH range.

If the project is for continuous treatment of inflow to a lake, MPCA has required a National Pollutant Discharge Elimination System / State Disposal System (NPDES/SDS) Permit. The permit requires monitoring and reporting of the inflow and outflow (if applicable) for phosphorus and the chemical used to reduce the nutrient. Permits last for five years before expiring, and application and annual permit fees apply.


Cooke, Dennis G. Restoration and Management of Lakes and Reservoirs, Third Edition. Lewis Publishers, 2005.

Cooke, G.D., R.T. Heath, R.H. Kennedy, and M.R. McComas. 1978. Effects of diversion and alum application on two eutrophic lakes. EPA-600/3-81-012. Freemen, R.A. and W.H. Everhart. 1971.

Toxicity of Aluminum Hydroxide Complexes in neutral and basic media to rainbow trout. Transactions of the American Fisheries Society 100: 644-658. Kennedy, R. and Cooke, G. 1982.

Control of Lake Phosphorus with Aluminum Sulfate: Dose Determination and Application Techniques”. Water Resources Bulletin 18:389-395. Narf, R.P. 1990.

Interaction of Chrionomidae and Chaoboridae (Diptera) with aluminum sulfate treated lake sediments. Lake Reserv. Manage. 6: 33-42. Welch, E.B. and G.D. Cooke. 1999.

Effectiveness and longevity of phosphorus inactivation with alum. J. Lake and Reserv. Manag. 15:5-27.


For lake protection and restoration questions, please contact Pam Anderson at 651-757-2190 or  

For in-lake treatment system questions, please contact Elise Doucette at 651-757-2316 or or Dennis Wasley at 651-757-2809 or