In This Issue
Winter Issue of The Bridge on Sustainable Water Resources
December 15, 2011 Volume 41 Issue 4

Nutrient Control in Large-Scale U.S. Watersheds

Thursday, December 15, 2011

Author: David A. Dzombak

The Chesapeake Bay and Northern Gulf of Mexico

Hypoxic conditions in the Chesapeake Bay and northern Gulf of Mexico are examples of the challenges posed by large-scale nonpoint discharges of nutrients.

Nutrient contamination of surface waters, especially from nitrogen and phosphorus, has long been a major water-quality problem around the world. In the United States, nutrient contamination has created problems in lakes and coastal waters, including Lake Erie, the Chesapeake Bay, the northern Gulf of Mexico, and many other locations.

Although nutrients are necessary to support aquatic ecosystems, excessive amounts can cause serious damage. Nutrients in runoff from municipal, industrial, and agricultural sources stimulate the growth of algae, which, upon dying, are degraded by bacteria that consume oxygen in the water. This can result hypoxia (i.e., low oxygen conditions sometimes referred to as “dead zones”). Because of the large-scale impacts of nutrient contamination, the National Academy of Engineering has identified management of the nitrogen cycle as one of the 14 grand challenges for engineering in the 21st century (NAE, 2011).

This article provides an overview of the nutrient-control challenge for large-scale watersheds, the impacts of nutrient loadings on water quality in the Chesapeake Bay and northern Gulf of Mexico, and efforts to reduce nutrient inputs in these two prominent bodies of water. The technical and regulatory challenges in addressing diffuse, “nonpoint” sources of nutrients are also discussed.

The Clean Water Act and Nonpoint Source Control

The primary source of nutrients—nitrogen and phosphorus—found in lakes, rivers, and coastal waters of the United States and elsewhere around the world is rainfall-induced runoff from agricultural lands to which nutrient compounds have been added as fertilizer. Control of these and other nonpoint sources, especially over large areas, poses technical and administrative challenges. In the United States, the administrative challenges might be as significant as the technical challenges, due in large part to limitations in the Clean Water Act, the major national law that governs protection of surface water quality.

Passed in 1972 and amended in 1977 and 1987, the Clean Water Act was a monumental achievement for the United States. The law put into place a combination of regulations, funding for treatment systems, and administrative controls that have resulted in significant reductions in water pollution and the restoration of many polluted bodies of water (ASIWPCA, 2004).

The law was the result of years of development and negotiations weighing the needs of states for flexibility in addressing particular kinds of water systems and water-quality issues against national interests and the need for basic levels of consistency for all states (ASIWPCA, 2004; Craig, 2004; Houck, 2002).

The primary focus of the Clean Water Act is on controlling point source discharges (i.e., discharges from discrete conveyances, such as channels and pipes), and regulatory efforts in the first 25 years after passage of the law were predominantly focused on discharges of municipal and industrial wastewater. In the 1970s and 1980s, the nation invested in the construction of many municipal wastewater treatment plants through a construction-grant program that was part of the Clean Water Act. A system of regulatory permitting of point source discharges was also instituted, and within two decades, tremendous progress was made in bringing pollution from point sources under control.

However, control of nonpoint sources—such as runoff from urban and agricultural land—is a much more complex and difficult challenge. The Clean Water Act provides assistance for states to study nonpoint source pollution and implement programs to mitigate nonpoint discharges. However, the law does not include regulations or enforcement mechanisms for nonpoint source control.

The relatively weak provisions in the law for addressing nonpoint sources of water pollution represent a basic shortcoming. Nevertheless, the existing nonpoint source provisions do provide a framework for understanding the contributions of nonpoint sources to the overall quality of a body of water and for targeting the highest priority sources for action.

Today, provisions in the Clean Water Act for characterizing and mitigating nonpoint sources, for assessing water quality, and for setting goals for contaminant load limits are a starting point for taking on large-scale issues of nonpoint source contamination, such as nutrients in runoff. Hypoxic conditions in the Chesapeake Bay and northern Gulf of Mexico are two high-profile examples of the challenges posed by large-scale nonpoint source discharges of nutrients.

Nutrient Inputs to Surface Waters

The nutrients of most concern for water quality are dissolved species of nitrogen and phosphorus, especially nitrogen, which is more soluble than phosphorus and hence has greater potential for aqueous transport. The primary concern about both nutrients is that they enrich waters and stimulate algal production.

Algae use dissolved inorganic carbon (CO2) and nutrients in the presence of light to form plant protoplasm, increase algal biomass, and release oxygen.
description for Dzombak light formula

In this process (photosynthesis), nutrients are incorporated into the synthesized biomass.

Algal growth impacts water quality when algae die and algal biomass is degraded by bacteria, which consume oxygen in the process. Aerobic biodegradation of organic matter in algal biomass involves conversion of organic carbon back into inorganic carbon, CO2.

description for Dzombak bacteria forula

The big problem is the consumption of oxygen by bacteria in the conversion process. Thus, as algal biomass is degraded, oxygen dissolved in the water is used up, usually at a much faster rate than it can be resupplied from the atmosphere.

In many respects, the level of dissolved oxygen is the most important chemical parameter in determining the ecological health of waters. The level of dissolved oxygen is a very sensitive water quality parameter in that the solubility of oxygen is low, about 10 milligrams per liter at 20°C. Thus, it does not take much aerobic biodegradation of organic matter to use up most or all of the oxygen, causing hypoxia.

Hypoxia is a condition of a low concentration of dissolved oxygen in water. At concentrations of less than about 4 milligrams per liter, many types of fish and other aquatic organisms cannot be sustained. Thus, decreasing dissolved oxygen changes the nature of an aquatic system dramatically.

Sources of Nutrient Discharges

Nutrient loading in surface waters comes from both point and nonpoint sources. Municipal wastewater treatment plants, which are common point sources, discharge nitrogen and phosphorus species. However, their contribution to overall loading depends on the local conditions, such as the size of the body of water receiving the discharge.

Wastewater treatment facilities may be dominant sources of nutrients in one section of a river or a lake, but for large watersheds, they are often relatively small contributors of nutrients compared to runoff from agricultural lands. In the Mississippi River, for example, about 90 percent of the nitrogen load that reaches the Gulf of Mexico comes from nonpoint sources; the remaining 10 percent comes primarily from industrial and municipal point sources (NRC, 2008). Nutrients in storm-water runoff from urban environments (e.g., nutrients from fertilizers applied to lawns) also contribute to nutrient loading.

Runoff from nonpoint sources, whether in urban or agricultural environments, enters a body of water in a more distributed and diffuse way than discharges from point sources and thus is more difficult to control. In most large watersheds, runoff from agricultural lands, where large amounts of nitrogen and phosphorus are applied regularly to increase crop production, is the major nutrient source.

Another nonpoint source, although much less important than agricultural runoff, is deposition from the atmosphere. Emissions of nitrogen compounds to the atmosphere (e.g., ammonia and nitrogen oxides) can be washed out by rain, deposited in watersheds, and transported to receiving waters.


Discharge of large amounts of nutrients leads to hypoxia in lakes, streams, estuaries, and coastal waters. In this article, the focus is on coastal waters where nitrogen loadings are the most significant cause of hypoxic conditions.

The production and application of nitrogen- and phosphorus-bearing fertilizers in agriculture has increased dramatically in the last half-century. Thus, as a result of human activity, nitrogen loading to coastal waters is about six times higher than natural loadings (Howarth and Marino, 2006). In some cases it is 10 times higher or more relative to natural background levels (Howarth and Marino, 2006).

Figure 1

High-nutrient loading in coastal waters is a problem along much of the coastline of the United States, and also across the globe (Figure 1). Humans have perturbed the natural cycle of nitrogen by fixing it out of the atmosphere at much higher rates than occurs naturally, primarily for the production of ammonia (NH3), which is incorporated into fertilizers and eventually ends up in runoff as nitrate (NO3) (NRC, 2000).

Restoration Efforts in the Chesapeake Bay

Hypoxia in the Chesapeake Bay as a result of nutrient inputs is a longstanding problem. Figure 2 shows the extent to which low dissolved-oxygen levels (generally less than 4 to 5 milligrams per liter) existed in the Chesapeake Bay during the summer months from 2007 to 2009. As the figure shows, levels of dissolved oxygen were lower than desired in many of the tributaries as well as in the main body of the bay.

Figure 2

Hypoxia in the Chesapeake Bay has been investigated longer, and more resources have been expended on it, than for any other coastal water in the United States. In 1983, in cooperation with the Environmental Protection Agency (EPA), a multi-state agreement was put in place. Additional states joined later, and the partnership now involves six states, the District of Columbia, and EPA (CBP, 2011).

The partnership has focused on reducing nutrient and sediment loadings in the Chesapeake Bay with the goal of restoring bay grasses, various species of fish, blue crabs, and other aquatic life. This is a basin-wide effort that involves coordinated monitoring throughout the watershed and a central modeling effort to synthesize data and provide a framework for interpretation and informing decisions.

The Chesapeake Bay Program represents a model effort in the United States for addressing the challenge of nutrient pollution in coastal waters. Efforts have been ongoing for more than 25 years and have involved substantial investments of resources from all partners. Progress has been slow, which is frustrating to some, but it will necessarily take a long time to stabilize and reverse this large-scale water-quality problem that developed over a period of more than 200 years of changing land use and population increase in this large watershed.

Progress in the Chesapeake Watershed

The Chesapeake Bay Program has become the test case for the nation for learning how to address watershed-scale nutrient pollution under the Clean Water Act, from both a technical and administrative standpoint. The undertaking has been challenging and very expensive, but much has been learned and progress has been made.

The Chesapeake Bay Program has greatly improved our understanding of the sources of the most significant nutrient loadings to the bay. Figure 3 shows a map of the watershed indicating the relative impact on levels of dissolved oxygen of nutrient loadings from various areas. As Figure 3 shows, the Susquehanna River basin, which extends through Maryland, Pennsylvania, and into New York, is the most significant contributor of nutrient loadings, but not the only one.

  Figure 3

This information, developed through long-term monitoring and modeling, has provided a basis for setting goals for controlling nutrient levels in sub-watershed areas and establishing caps on the amount of nutrients released from different sub-watersheds in the basin. Nutrient control goals have been set for 9 major river basins in the Chesapeake Bay watershed, and related goals have been set for 20 tributary basins. At the state level, goals are further subdivided down to the level of individual farms.

In December 2010, under legal pressure from external groups, an agreement was reached by the partner states and EPA to establish specific total maximum daily loads (TMDLs) of nutrients and sediment (EPA, 2010). A TMDL is a tool established in the Clean Water Act for specifying maximum allowable discharge loads to achieve water quality goals and for assessing sources of loadings in a watershed for the purpose of reducing them and prioritizing the allocation of resources. Establishing TMDLs for nutrients and sediments in the bay provided a basis for determining maximum allowable (or cap) loads for various jurisdictions in the Chesapeake Bay watershed.

In fact, the Clean Water Act requires the establishment of TMDLs once water quality impairment has been demonstrated. However, TMDLs are not the same as enforceable limits under a discharge permit. Instead, they are meant to provide a basis for establishing watershed implementation plans to achieve water quality goals, including load caps for all sub-watersheds.

The TMDL concept and process were included in the original Clean Water Act passed in 1972, but they have only been put to use in earnest since the late 1990s as a result of legal actions requiring EPA and states to do so (Houck, 2002).

The Chesapeake Bay TMDL of December 2010 has led to a great deal of scientific and regulatory progress, as well as lawsuits among the partners, and it will take some time for the nature and effectiveness of the responses to become clear. What is clear, however, is that the implementation of the TMDL for the Chesapeake Bay is a formative experience for learning how large-scale nonpoint source pollution can be addressed under the Clean Water Act.

Hypoxia in the Northern Gulf of Mexico

The northern Gulf of Mexico has large areas of hy-poxia as a result of nitrogen from the Mississippi River basin. Figure 4 shows the extent of hypoxia in the northern Gulf of Mexico in summer 2010 (EPA, 2011). Although the area of low dissolved oxygen has been expanding consistently since monitoring began, to date, no coordinated effort to remediate the hypoxia problem in the northern Gulf of Mexico has been initiated. Nevertheless, the need for taking action is clear, and various groups have put forward ideas for doing so (NRC, 2008).

Figure 4

Gaining control of nutrient and sediment inputs in the northern Gulf of Mexico is a more complex problem than for the Chesapeake Bay because of the enormous size of the Mississippi River basin, which covers more than half of the continental United States. In addition, like the Chesapeake Bay basin, the Mississippi River basin has undergone extensive modifications, including the development of large cities on the main stem Mississippi River and its tributaries and, more distinctively, massive clearing of land and intensive agriculture in the basin.

The U.S. Geological Survey has compiled water-quality data on nutrients in the Mississippi River and its tributaries and developed a spatial regression model to estimate loadings from sub-watersheds that contribute to the tributary and main stem sections of the river. Figure 5 shows the estimated nitrogen delivery to the Gulf of Mexico from land areas throughout the Mississippi River basin; these estimates are based on analyses of water-quality data by the SPARROW (spatially referenced regressions on watershed attributes) model (Alexander et al., 2008).

The shading in Figure 5 indicates areas with relatively high and relatively low loadings, in terms of estimated total nitrogen yields in kilograms per square kilometer delivered to the Gulf of Mexico. A similar analysis was performed for phosphorus loadings (Alexander et al., 2008).

Figure 5

Figure 6 shows how nutrient loading to the Gulf of Mexico from the Mississippi River has increased over time. The graph shows nitrate (NO3) loading in millions of metric tons per year based on measurements of nitrate concentration, and volumetric flow rates at a particular sampling location along the Mississippi River in southern Louisiana.

Figure 6

Flow measurements, also shown on the graph, illustrate that annual flows vary around an average value. In contrast, nitrogen loading has increased steadily over time, which is reflected in the rising levels of nitrate concentrations.

Clearly, the amount of nitrogen discharged to the Mississippi River and the northern Gulf of Mexico has been increasing. To shrink the size of the hypoxic region will require stopping and reversing this trend, an enormous challenge considering that this is the largest watershed in the nation.

Charting a Path Forward

The National Research Council has conducted three studies and issued three reports on water quality in the Mississippi River and the nutrient-control issue (NRC, 2008, 2009, 2010). The first study (NRC, 2008) focused on Mississippi River water quality issues in general and how well the Clean Water Act is protecting and restoring water quality in the river. The two subsequent studies (NRC, 2009, 2010) focused on particular science, engineering, and institutional challenges to reducing nutrient pollutant loads throughout the Mississippi River basin. The challenge of controlling water pollution largely from nonpoint sources in a large watershed is magnified for the Mississippi River basin because of its size and because of the large number of states that must participate in coordinated action to address the problem effectively.

As discussed above, the primary mechanism in the Clean Water Act for addressing nonpoint sources is through the TMDL process, which involves studying, on a watershed scale, the sources of loads of specific contaminants or contaminant groups. Such an integrative framework is critical to developing a system-wide view of the location and magnitude of sources, a plan for prioritizing the sources, and plans to reduce inputs from the most significant ones.

The data on water quality and hydrology from across the watershed can be used to develop and calibrate watershed-scale water-quality models for interpreting monitoring data and making projections of the effects of implementing various control options. System-scale modeling has been a critical tool for evaluating data and forecasting water quality for the Chesapeake Bay watershed (NRC, 2011).

Lack of Coordination

In contrast to the coordinated monitoring and modeling efforts for the Chesapeake Bay, no coordinated monitoring efforts among states in the Mississippi River basin or system-wide modeling has been initiated. In addition, although several federal agencies maintain programs that include some monitoring of water quality in the Mississippi River watershed and the northern Gulf of Mexico, no single federal program is monitoring water quality and collecting data for the river as a whole.

The National Oceanic and Atmospheric Administration collects water quality data for the Gulf of Mexico; the U.S. Army Corps of Engineers oversees the federal-state Environmental Management Program for the upper Mississippi River; and the U.S. Geological Survey has collected water-quality data for many years at specific Mississippi River locations under various monitoring programs. Thus, the monitoring and management of water quality in the Mississippi River is fragmented, with different agencies conducting programs with a variety of goals (NRC, 2008).

A Strategy for Coordinated Efforts

The NRC (2008) committee that evaluated the monitoring and management of water quality in the Mississippi River from a system-level perspective concluded that “there is a clear need for federal leadership in system-wide monitoring of the Mississippi River” and that “the EPA should take the lead in establishing a water quality data sharing system.” The committee argued that EPA is best positioned, and indeed obligated by the Clean Water Act, to facilitate better interstate collaboration and improve delivery of Clean Water Act programs, such as permitting, monitoring, and conducting water-quality assessments.

To advance nutrient control in the Mississippi River basin, NRC (2008) recommended that EPA develop water-quality criteria for nutrients in the Mississippi River and northern Gulf of Mexico and ensure that states in the basin also establish water-quality standards (i.e., designated uses and water quality criteria) as well as TMDLs to protect against excessive nutrient pollution. The NRC (2008) committee also recommended that EPA ultimately develop a federal TMDL, or the functional equivalent, for the Mississippi River and northern Gulf of Mexico through a process similar to the one developed for the Chesapeake Bay.

Because runoff from agricultural lands is the main contributor of nutrient loadings to the Mississippi River, reducing those inputs will be a critical goal that will require implementing effective management practices. Existing U.S. Department of Agriculture (USDA) programs already provide technological and financial support for implementing nonpoint source control in agriculture. However, these programs will have to be coordinated with efforts by EPA and state water-quality agencies to realize their potential for improving water quality. Examples of relevant USDA programs include the Conservation Reserve Program (CRP), Environmental Quality Improvement Program (EQIP), and Conservation Security Program (CSP).

In the first two NRC reports (2008, 2009), the authoring committees recommended that (1) USDA conservation programs be focused aggressively on runoff from areas with high nutrient input and (2) that EPA and USDA combine their efforts to reduce impacts from agriculture on water quality in the Mississippi River and northern Gulf of Mexico.

NRC (2009) outlined a number of specific actions that could be undertaken jointly and separately by USDA and EPA to make a start on the large-scale challenge of reducing nutrient discharges into the waters of the Mississippi River basin. Some of these activities have been initiated, notably a USDA program (described below) focused on the highest priority watersheds in the basin in terms of nutrient loadings.

The Mississippi River Basin Healthy Watersheds Initiative

The USDA Mississippi River Basin Healthy Watersheds Initiative (MRBI), established in 2009, is a four-year, $320 million program that targets 41 watersheds in the Mississippi River basin. The program is designed to promote improvements in nutrient management and water quality. Considering the provisions of the Clean Water Act and the responsibilities of EPA, close collaboration between USDA and EPA will be essential to the success of this program.

The authoring committee of the third NRC report (2010) noted that EPA support for MRBI could promote research and learning important for informing future management decisions. Thus MRBI could be an important first step toward an action-oriented, basin-wide, adaptive strategy for improving nutrient control in the vast Mississippi River basin.


Excess nutrient loading of nitrogen and phosphorus is a problem in surface and coastal waters of the United States and around the world. The primary impact is low levels of dissolved oxygen, or hypoxia, which has harmful effects on aquatic ecosystems and commercial fisheries. Hypoxic conditions in large areas of the Chesapeake Bay and the northern Gulf of Mexico from riverine loadings of nutrients are two prominent examples in the United States. Nonpoint sources, primarily runoff from agricultural lands, are the primary contributors to nutrient loadings.

The Chesapeake Bay Program, established in 1983, is a partnership of six basin states, the District of Columbia, and EPA that has become the model effort in the United States for addressing the challenge of nutrient pollution in coastal waters in the framework of the Clean Water Act. Despite substantial investments of resources by all partners, progress has been frustratingly slow.  However, it must be recognized that it will take a long time to stabilize and reverse this large-scale problem that developed over the course of more than 200 years of changes in land use in this large watershed.

The challenge of controlling nonpoint sources of nutrients is magnified for the Mississippi River watershed because of its very large size and the large number of states that must coordinate their efforts. In several recent reports, the NRC concluded: (1) there is a clear need for federal leadership in system-wide monitoring of the Mississippi River and system-wide modeling and (2) EPA is the government entity best positioned to facilitate interstate collaboration and provide basin-wide coordination.

In addition, considering that runoff from agricultural lands is the dominant contributor to nutrient loading, USDA will be a vital participant in efforts to improve nutrient control in the Mississippi River basin. The Mississippi River Basin Healthy Watersheds Initiative, a USDA program, could represent an important first step toward an action-oriented, basin-wide, adaptive strategy for reaching that goal.


Alexander, R.B., R.A. Smith, G.E. Schwarz, E.W. Boyer, J.V. Nolan, and J.W. Brakebill. 2008. Differences in phosphorous and nitrogen delivery to the Gulf of Mexico from the Mississippi River Basin. Environmental Science and Technology 42: 822–830.

ASIWPCA (Association of State and Interstate Water Pollution Control Administrators). 2004. Clean Water Act Thirty-Year Retrospective. Washington, D.C.: ASIWPCA.

CBP (Chesapeake Bay Program). 2011. Chesapeake Bay Program: A Watershed Partnership. Available online at

Craig, R.K. 2004. The Clean Water Act and the Constitution. Washington, D.C.: Environmental Law Institute.

EPA (U.S. Environmental Protection Agency). 2003. Setting and Allocating the Chesapeake Bay Basin Nutrient and Sediment Loads: The Collaborative Process, Technical Tools, and Innovative Approaches. Principal authors R. Koroncai, L. Linker, J. Sweeney, and R. Baiuk. U.S. Environmental Protection Agency, Region III, Chesapeake Bay Program Office, Annapolis, MD. Available online at 19713.pdf.

EPA. 2010. Fact Sheet: Chesapeake Bay Total Maximum Daily Load (TMDL): Driving Actions to Clean Local Waters and the Chesapeake Bay. Available online at BayTMDLFactSheet 8_6.pdf.

EPA. 2011. Hypoxia 101. U.S. Environmental Protection Agency, Mississippi River–Gulf of Mexico Watershed Nutrient Task Force. Available online at hypoxia10 1.cfm.

Goolsby, D.A., and W.A. Battaglin. 2000. Nitrogen in the Mississippi River Basin—Estimating Sources and Predicting Flux to the Gulf of Mexico. Fact Sheet 135-00. USGS Kansas Water Science Center. Available online at

Houck, O.A. 2002. The Clean Water Act TMDL Program: Law, Policy, and Implementation. Washington, D.C.: Environmental Law Institute.

Howarth, R.W., and R. Marino. 2006. Nitrogen as the limiting nutrient for eutrophication in coastal marine ecosystems: evolving views over three decades. Limnology and Oceanography 51(1): 364–376.

NAE (National Academy of Engineering). 2011. Grand Challenges for Engineering. Available online at

NRC (National Research Council). 2000. Clean Coastal Waters: Understanding and Reducing the Effects of Nutrient Pollution. Washington, D.C.: National Academies Press.

NRC. 2008. Mississippi River Water Quality and the Clean Water Act: Progress, Challenges, and Opportunities. Washington, D.C.: National Academies Press.

NRC. 2009. Nutrient Control Actions for Improving Water Quality in the Mississippi River Basin and Northern Gulf of Mexico. Washington, D.C.: National Academies Press.

NRC. 2010. Improving Water Quality in the Mississippi River Basin and Northern Gulf of Mexico: Strategies and Priorities. Washington, D.C.: National Academies Press.

NRC. 2011. Achieving Nutrient and Sediment Reduction Goals in the Chesapeake Bay: An Evaluation of Program Strategies and Implementation. Washington, D.C.: National Academies Press.


About the Author:David A. Dzombak is Walter J. Blenko Sr. University Professor of Environmental Engineering, Carnegie Mellon University, and an NAE member.