United States Office of Water (4303) EPA-821-B-01-001

Environmental Protection Washington, DC 20460 January 2001

Agency

Environmental Assessment of

Proposed Revisions to the

National Pollutant Discharge

Elimination System Regulation

and the Effluent Guidelines for

Concentrated Animal Feeding

Operations

Environmental Assessment of Proposed Revisions to the

National Pollutant Discharge Elimination System Regulation

and Effluent Limitations Guidelines for

Concentrated Animal Feeding Operations

Carol M. Browner

Administrator

J. Charles Fox

Assistant Administrator, Office of Water

Sheila E. Frace

Director, Engineering and Analysis Division

Donald F. Anderson

Chief, Commodities Branch

Patricia Harrigan

Environmental Assessor

Engineering and Analysis Division

Office of Science and Technology

U.S. Environmental Protection Agency

Washington, D.C. 20460

January 2001
ii

ACKNOWLEDGMENTS AND DISCLAIMER

This report has been reviewed and approved for publication by the Engineering and Analysis

Division, Office of Science and Technology. This report was prepared with the support of Abt

Associates Inc., under the direction and review of the Office of Science and Technology. Dr.

Gerald D. Stedge served as Abt Associates’ Principal Investigator and Project Manager. Dr.

Stedge was assisted by Mr. Peter Eglington, Ms. Amy Benson, Ms. Laura Kirk and Ms. Diane

Ferguson.

Neither the United States government nor any of its employees, contractors, subcontractors, or

other employees makes any warranty, expressed or implied, or assumes any legal liability or

responsibility for any third party’s use of, or the results of such use of, any information,

apparatus, product, or process discussed in this report, or represents that its use by such a third

party would not infringe on privately owned rights.
iii

CONTENTS

EXECUTIVE SUMMARY . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix

1. INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1

1.1 BACKGROUND . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1

1.2 OVERVIEW OF ANIMAL FEEDING OPERATIONS . . . . . . . . . . . . . . . . . . 1-3

1.3 ORGANIZATION OF REPORT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-6

2. ANIMAL WASTE CHARACTERISTICS AND TRANSPORT TO SURFACE

WATERS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1

2.1 QUANTITY OF MANURE GENERATED . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1

2.1.1 Total Manure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1

2.1.2 Recoverable Manure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-2

2.2 POLLUTANTS OF CONCERN . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-7

2.2.1 Nutrients . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-7

2.2.2 Ammonia . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-10

2.2.3 Pathogens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-12

2.2.4 Organic Matter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-12

2.2.5 Salts and Trace Elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-14

2.2.6 Antibiotics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-15

2.2.7 Hormones . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-15

2.2.8 Other Pollutants of Concern . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-15

2.3 TRANSPORT OF MANURE POLLUTANTS TO SURFACE WATER . . . . 2-16

2.3.1 Surface Discharges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-16

2.3.2 Other Discharges to Surface Waters . . . . . . . . . . . . . . . . . . . . . . . . . . 2-18

2.3.3 Pollutant-specific Transport . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-20

3. POTENTIAL HAZARDS FROM AFO POLLUTANTS . . . . . . . . . . . . . . . . . . . . . . . 3-1

3.1 PRIMARY NUTRIENTS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2

3.1.1 Ecology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2

3.1.2 Human Health . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4

3.2 AMMONIA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-6

3.2.1 Ecology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-6

3.2.2 Human Health . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-6

3.3 PATHOGENS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-7

3.3.1 Ecology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-7

3.3.2 Human Health . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-7

3.4 ORGANIC MATTER . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-12

3.4.1 Ecology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-12

3.4.2 Human Health . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-13

3.5 SALTS AND TRACE ELEMENTS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-13

3.5.1 Ecology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-13

3.5.2 Human Health . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-14

3.6 SOLIDS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-15

3.7 ANTIBIOTICS AND ANTIBIOTIC RESISTANCE . . . . . . . . . . . . . . . . . . . 3-15
iv

3.8 HORMONES AND ENDOCRINE DISRUPTION .................... . 3-16

3.9 OTHER POLLUTANTS OF CONCERN ........................... . 3-16

3.9.1 Gas Emissions .......................................... . 3-16

3.9.2 Particulates ............................................. . 3-17

3.9.3 Pesticides .............................................. . 3-17

4. NATIONAL AND LOCAL IMPACTS OF ANIMAL AGRICULTURE .......... . 4-1

4.1 NATIONAL WATER QUALITY INVENTORY RESULTS ............ . 4-1

4.2 NATIONAL ANALYSES OF NUTRIENT CONTRIBUTIONS .......... . 4-3

4.2.1 1994 USGS Study on Nitrogen Production from Various Sources ... . 4-3

4.2.2 1998 USDA Study of Nitrogen and Phosphorus Production Relative to

Crop Uptake Potential ..................................... . 4-6

4.2.3 1997 USGS Modeling Study of Nitrogen and Phosphorus Loadings to

Surface Waters .......................................... . 4-12

4.3 NATIONAL ANALYSIS OF SHELLFISH BED IMPAIRMENT ........ . 4-17

4.4 LOCAL IMPACTS ............................................ . 4-17

4.4.1 Lake Eucha ............................................. . 4-61

4.4.2 The Chino Basin ........................................ . 4-61

4.4.3 Lake Waco and the Bosque River Watershed .................. . 4-62

4.5 CASE STUDY SUMMARY ..................................... . 4-63

5. EFFECTS OF THE PROPOSED REGULATIONS .......................... . 5-1

5.1 POTENTIAL BENEFITS FROM POLLUTANT REDUCTIONS ........ . 5-1

5.2 REPORTED BENEFITS OF ANIMAL WASTE MANAGEMENT AND

RELATED NON-POINT SOURCE MEASURES IN SELECTED

WATERSHEDS ................................................ . 5-5

5.2.1 Benefits of Single Practices ................................ . 5-5

5.2.2 Benefits of Multiple Practices ............................... . 5-6
v

EXHIBITS

EXHIBIT 1-1

Industry Consolidation of Animal Feeding Operations, 1978 - 1992 . . . . . . . . . . . . . . 1-4

EXHIBIT 1-2

Increase in the Average Number of Animal Units per Operation, 1978-1992 . . . . . . . 1-4

EXHIBIT 1-3

Farms, Number of Head, and Cropland, by Confined Animal Facility Size, 1992 . . . . 1-5

EXHIBIT 2-1

Manure Production by Both Livestock and Humans . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-2

EXHIBIT 2-2

Fraction of Recoverable Manure, by Animal and by State . . . . . . . . . . . . . . . . . . . . . . 2-4

EXHIBIT 2-3

Estimated Recoverable Manure and Manure Nutrients Generated by Sector . . . . . . . . 2-6

EXHIBIT 2-4

Primary Nutrients in Both Livestock and Human Manures . . . . . . . . . . . . . . . . . . . . . . 2-8

EXHIBIT 2-5

The Nitrogen Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-9

EXHIBIT 2-6

The Phosphorus Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-11

EXHIBIT 2-7

Coliform Bacteria in Manure (colonies per cubic foot of manure, as excreted) . . . . . 2-12

EXHIBIT 2-8

Reported BOD5 and COD Concentrations for Manures and Domestic Sewage . . . . . 2-14

EXHIBIT 3-1

Some Diseases and Parasites Transmittable to Humans from Animal Manure . . . . . . . 3-8

EXHIBIT 3-2

Etiology of Waterborne Disease Outbreaks Causing Gastroenteritis 1989-1996 . . . . 3-10

EXHIBIT 4-1

Five Leading Sources of Water Quality Impairment in the United States . . . . . . . . . . . 4-1

EXHIBIT 4-2

Summary of U.S. Water Quality Impairment Survey . . . . . . . . . . . . . . . . . . . . . . . . . . 4-2

EXHIBIT 4-3

Percent of Total Agricultural Impairment Contributed by Animal Agriculture . . . . . . 4-2

EXHIBIT 4-4

Five Leading Causes of Water Quality Impairment in the United States . . . . . . . . . . . 4-3

EXHIBIT 4-5

Proportions of Nitrogen Sources in Selected Watersheds (1987 Base Year) . . . . . . . . 4-5

EXHIBIT 4-6

Estimated Manure Nitrogen Production from Confined Livestock . . . . . . . . . . . . . . . . 4-8

EXHIBIT 4-7

Estimated Manure Phosphorus Production from Confined Livestock . . . . . . . . . . . . . . 4-9

EXHIBIT 4-8

Potential for Nitrogen Available from Animal Manure to Meet or Exceed

Uptake and Removal on Non-Legume, Harvested Cropland and Hayland . . . . . . . . . 4-10
vi

EXHIBIT 4-9

Potential for Phosphorus Available from Animal Manure to Meet or Exceed

Uptake and Removal on Non-Legume, Harvested Cropland and Hayland ........ . 4-11

EXHIBIT 4-10

Predicted Local Nitrogen Yield in Hydrologic Cataloging Units ............... . 4-13

EXHIBIT 4-11

Predicted Local Total Phosphorus Yield in Hydrologic Cataloging Units ........ . 4-14

EXHIBIT 4-12

Predicted Percentage Contribution of Animal Waste to Local

Total Nitrogen Export from Hydrologic Cataloging Units .................... . 4-15

EXHIBIT 4-13

Predicted Percentage Contribution of Animal Waste to Local

Total Phosphorus Export from Hydrologic Cataloging Units .................. . 4-16

EXHIBIT 4-14

Shellfish Beds Impaired by Feedlots ..................................... . 4-17

EXHIBIT 4-15

Description of Environmental Incidents and Impacts Tables .................. . 4-18

EXHIBIT 4-16

Documented Discharges from Swine Operations to Surface Waters ............. . 4-19

EXHIBIT 4-17

Documented Human Health Related Impacts from Swine Operations ........... . 4-29

EXHIBIT 4-18

Documented Ecological, Recreational, and Other Impacts from Swine Operations . . 4-30

EXHIBIT 4-19

Documented Discharges from Poultry Operations to Surface Waters ............ . 4-37

EXHIBIT 4-20

Documented Human Health Related Impacts from Poultry Operations .......... . 4-39

EXHIBIT 4-21

Documented Ecological, Recreational, and Other Impacts from Poultry Operations . 4-40

EXHIBIT 4-22

Documented Discharges from Beef and Dairy Operations to Surface Waters ..... . 4-41

EXHIBIT 4-23

Documented Human Health Related Impacts from Beef and Dairy Operations .... . 4-49

EXHIBIT 4-24

Documented Ecological, Recreational, and Other Impacts from Beef and Dairy

Operations ......................................................... . 4-50

EXHIBIT 4-25

Documented Discharges to Surface Waters from Operations with Unspecified or Multiple

Animal Types ....................................................... . 4-51

EXHIBIT 4-26

Documented Human Health-Related Impacts from Operations with Unspecified or

Multiple Animal Types ............................................... . 4-57
vii

EXHIBIT 4-27

Documented Ecological, Recreational, and Other Impacts from Operations with

Unspecified or Multiple Animal Types ................................... . 4-58

EXHIBIT 5-1

Anticipated Benefits of the CAFO Proposed Regulations ...................... . 5-2
viii
ix

EXECUTIVE SUMMARY

States report that agriculture is the leading source of impairment in the nation’s surveyed rivers

and lakes. In the states that categorized sources of impacts to rivers in 1998, intensive animal

operations accounted for over 15 percent of the total impairment due to agriculture. Manure and

other animal wastes from these animal feeding operations (AFOs) can result in human health and

potentially significant environmental impacts. Such impacts continue to cause concern despite

federal effluent limitation guidelines that address feedlots, which have been in place since 1974. 

Since the EPA promulgated the original effluent guidelines, there have been persistent reports of

discharge and runoff of manure pollutants reaching surface and groundwater and resulting in fish

kills and other adverse impacts.

Animal production has undergone significant changes in the past several decades. Between 1987

and 1992, the total number of animal units increased by about 4.5 million (approximately 3

percent). At the same time, the number of facilities has decreased, indicating a consolidation

within the livestock industry.

Animal Waste Characteristics

Beef, dairy, swine, and poultry operations generated a total of 291 billion pounds of manure

(weight of dry-state or dried manure) in 1997. This figure represents recoverable and nonrecoverable manure. Recoverable manure is generally indicative of confined operations, because

it is waste that is contained within the production area. The U.S. Environmental Protection

Agency (EPA) estimates the amount of manure that is recoverable from each of the four animal

sectors addressed by the guidelines to be beef (16 percent), dairy (76 percent), swine (92

percent), and poultry (98 percent).

Animal waste contains a number of pollutants. The presence and concentration of these

pollutants may vary depending on the animal species and other factors, such as animal size,

maturity, and health, as well as the composition (e.g., protein content) of animal feed.

Nitrogen, an essential nutrient required by all living organisms, exists in fresh manure in organic

and ammonium forms. Nitrogen can transform to nitrate, and it is then water soluble and highly

mobile in the environment. When farmers apply excess manure as fertilizer to crops, nitrates

may run off into surface water and may leach to groundwater. Like nitrogen, phosphorus also

exists in animal waste. As animal waste ages, the organic phosphorus mineralizes to inorganic

phosphate compounds and becomes available to plants. Organic phosphorus compounds are

generally water soluble and may leach through soil to groundwater and run off into surface

waters. Inorganic phosphorus attaches to soil particles and may reach surface waters through

erosion.

The ammonia content of fresh manure varies among animal species and changes as the manure

ages. Ammonia content may increase as organic matter breaks down; it may decrease when

volatilization occurs or when nitrate oxidizes to nitrite under aerobic conditions. A major

method of transport of ammonia is through atmospheric deposition from airborne emissions.
x

Livestock manure contains many pathogens, including protozoa, bacteria, and viruses. Multiple

species of pathogens may be transmitted directly from a host animal’s manure and may increase

in number in a waterbody due to loadings of animal manure nutrients. Pathogen contamination

from AFOs includes discharges directly to surface waters and discharges from leaching lagoons,

and can reach surface waters and groundwater. Soil type, manure application rate, and soil pH

are dominating factors in the survivability of bacteria. Type of storage and length of storage also

affect bacterial survivability.

Organic compounds in animal manure can enter water directly from feedlots and land application

sites. They then undergo decomposition by aquatic bacteria and other microorganisms. In the

process, the organisms consume dissolved oxygen, reducing the amount available for aquatic

animals. Measures that indicate presence of the organic compounds in manure are the

biochemical oxygen demand (BOD) and the chemical oxygen demand (COD). Even after

treatment, these measures are much higher for animal waste than for municipal treated waste.

Several other pollutants can reach surface water and groundwater. Dissolved mineral salts and

several trace elements (including arsenic, copper, selenium, and zinc) can reach surface waters

via discharges directly to the waterbody as well as runoff from land application sites and can

leach into groundwater. Although present in small amounts in manure, trace elements may

bioconcentrate in plants and animal tissues and persist in the environment. The degradation of

animal wastes by microorganisms may produce gases with strong odors. Particulate emissions,

pesticides, antibiotics, and hormones also exist in animal waste and may impact the environment.

Human Health Hazards Associated with Animal Wastes

Many constituents of animal waste, including primary nutrients, pathogens, salts, and gases, can

affect human health. Elevated nitrate levels in drinking water are a major health concern. In

particular, infants are at risk from nitrate poisoning (also referred to as methemoglobinemia or

“blue baby syndrome”), which results in oxygen starvation. Nitrate poisoning may increase the

risk of birth defects and miscarriages, and is potentially fatal.

Pathogens in animal waste cause many human diseases. These include salmonellosis,

cryptosporidiosis, giardiasis, cholera, typhoid fever, and polio. Humans may come into contact

with the pathogens via the fecal-oral route, inhalation, or consumption of contaminated water. 

The protozoan Cryptosporidium parvum is of particular concern because it is resistant to

conventional drinking water treatment. Cryptosporidium can produce gastrointestinal illness,

with symptoms such as severe diarrhea.

Salts in animal waste are also a human health hazard. At low levels, salts can increase blood

pressure in salt-sensitive individuals, increasing the risk of stroke and heart attack. Trace metal

elements in manure can also impact human health For example, while zinc (a feed additive) is a

requirement for human physiology, it may induce toxicity at elevated concentrations.

The primary gases associated with aerobic decomposition include carbon dioxide and ammonia. 

Gases associated with anaerobic conditions, which dominate in typical, unaerated animal waste
xi

lagoons, include methane, carbon dioxide, ammonia, hydrogen sulfide, and over 150 other

compounds. Many of the end products can produce negative impacts, including strong odors.

Ecological Effects Associated with Animal Wastes

Animal waste can also have an effect on the natural ecosystem. Perhaps the most documented

impact of nutrient pollution is the increased surface water eutrophication (nutrient enrichment)

and its effects on aquatic ecosystems. Eutrophication causes the enhanced growth and

subsequent decay of algae, which can lower dissolved oxygen content of a waterbody to levels

insufficient to support fish and invertebrates. In some cases, this situation can produce large

areas devoid of life because of a lack of sufficient dissolved oxygen. An example of this is the

“Dead Zone,” a 10,000 km2

 area in the Gulf of Mexico. Researchers believe the Dead Zone is

caused by excess chemical fertilizer; however, nutrients from animal waste have also contributed

to the problem. Eutrophication may increase the incidence of harmful algal blooms, which

release toxins as they die and can severely impact wildlife as well as humans.

Parasites, bacteria, and viruses in animal waste may be harmful to wildlife. Certain bacteria in

livestock waste cause avian botulism and avian cholera, which have killed thousands of

migratory waterfowl. Shellfish can concentrate a broad range of microorganisms in their tissues,

providing a pathway for pathogen transmission to predator organisms. 

Ammonia is highly toxic to aquatic life and is a leading cause of fish kills. It is of environmental

concern because it exerts a direct oxygen demand on the receiving water as it breaks down. 

Ammonia loadings can contribute to accelerated eutrophication of surface waters. Also, organic

matter in surface waters supports increased microbial population and activity, and as these

microorganisms degrade the organic matter, the amount of dissolved oxygen available to other

aquatic organisms decreases.

Salts from manure can impact the ecosystem. In fresh water, increasing the salinity can disrupt

the balance of the ecosystem. On land, salts can become toxic to plants and deteriorate soil

quality by reducing permeability and generally impacting physical condition. Trace elements in

manure can impact plants, aquatic organisms, and terrestrial organisms. For example, metals

such as zinc (a feed additive) can accumulate at high concentrations in soil and become toxic to

plants.

National and Local Impacts from Animal Agriculture

Several analyses have estimated nationwide impacts from animal operations. First, in an analysis

of nitrogen sources (including manure, fertilizers, point sources, and atmospheric deposition) in

107 U.S. watersheds, the U.S. Geological Survey (USGS) found that proportions of nitrogen

originating from various sources differ according to climate, hydrologic conditions, land use,

population, and physical geography (Puckett, 1994). In several watersheds (particularly in the

South and Northeast), manure nitrogen accounts for a large portion of the total nitrogen added to

the watershed.
xii

In a second analysis, Lander et al. (1998) estimated the quantity of nutrients available from

confined livestock manure relative to crop growth requirements, by county, based on data from

the 1992 Census of Agriculture (USDC/Census Bureau, 1994). Recoverable manure nitrogen

exceeded crop system needs in 266 counties, and recoverable phosphorus exceeded crop system

needs in 485 counties.

A third analysis, by Smith et al. (1997), modeled transport of manure nutrients to surface water. 

The authors found that animal waste is a significant source (relative to other local sources) of instream nutrient concentrations in many watershed outlets, particularly in the central and eastern

United States. They also conclude that livestock waste contributes more than commercial

fertilizer application to total phosphorus exported from local sources (independent of upstream

sources).

The EPA has also documented local impacts. In Oklahoma, Lake Eucha has very high nutrient

loads associated with poultry production operations. In Florida, Lake Okeechobee has

experienced significant effects of phosphorus loadings from AFOs. In southeastern Delaware

and the Eastern Shore of Maryland, where poultry production is widespread, over 20 percent of

wells have nitrate levels exceeding the Maximum Contaminant Level (MCL) set by the EPA’s

Office of Ground Water and Drinking Water. Furthermore, localities have reported various

ecological impacts associated with releases from AFOs, including eutrophication and fish kills.

Over a 10-year period, localities have also reported nearly 100 individual fish kill events

associated with spills and discharges from AFOs.

This Report

Unlike environmental assessments prepared to support other effluent guidelines, this report

focuses on the qualitative impacts on human health and the environment associated with releases

of wastes to surface water from concentrated animal feeding operations (CAFOs). The EPA is

not currently able to quantitatively evaluate all human health and ecosystem benefits associated

with water quality improvements from reduced releases of CAFO wastes. The EPA is even more

limited in its ability to assign monetary values to those benefits. The economic benefit analysis

is available in the benefit report, titled “Environmental and Economic Benefits of the

NPDES/ELG CAFO Rules” and located in section 9.5 of the public record.

To present a sense of the scope of the problem, this report relies on state and federal information,

as well as news articles and data collected by environmental advocacy groups. While data from

government agencies are more reliable, the resources are not available to thoroughly track

CAFO-related releases of pollutants to the environment and the resulting environmental and

human health impacts. The intention of this more inclusive approach is to provide a sense of the

possible scope of the impacts until state and federal agencies can fully document them.
1

USDA’s National Resources Conservation Service calculated animal waste figures using the 1997 Census

of Agriculture (USDA/NASS, 1999) and the procedures in Lander et al. (1998).

1-1

1. INTRODUCTION

1.1 BACKGROUND

Animal waste can have a negative impact on surface water, ground water, soil, and air. While

there are many sources of water pollution, states report that agriculture is the leading source of

impairment in the nation’s surveyed rivers and lakes. Furthermore, nutrients and pathogens

account for a large percentage of contaminants found in the nation’s impaired waters (USEPA,

2000a).

Animal feeding operations (AFOs or feedlots) can pose a number of risks to human health and

the environment, mainly because of the significant amount of animal manure they generate. In

1997, farm animals generated an estimated 291 billion pounds (132 million metric tons) of

manure (dry-state basis) (USDA/NRCS, 2000).1 This figure far exceeds the estimated 49 billion

pounds (22 million metric tons) of human sanitary waste produced. Since the calculations handle

human and animal wastes differently, this comparison does not provide an indication of relative

environmental impact; however, it does indicate the significance of animal waste as a potential

source of pollution.

AFOs contribute manure pollutants to the environment via discharges directly into surface water,

surface runoff, leaching into soil and ground water, and volatilization/deposition. Sources of

these pollutants include animal confinement areas, pastures, treatment and storage lagoons,

manure stockpiles, and land application fields. Organic matter, ammonia, nutrients (particularly

nitrogen and phosphorus), solids, pathogens, and odorous compounds are the pollutants most

commonly associated with animal waste. Animal waste is also a source of salts and trace

elements, and to a lesser extent, pesticides, antibiotics, and hormones.

Manure can be a valuable fertilizer and soil conditioner, but in many cases it is applied in excess

of crop nutrient requirements due to manure nutrient ratios that differ from crop needs, and/or

lack of available nearby land on which to spread the manure. This problem has been of

increasing concern as more concentrated feeding operations maintain greater numbers of animals.

In surface water, the waste’s oxygen demand and ammonia content can directly result in fish

kills and reduced biodiversity. Solids can increase turbidity and suffocate benthic organisms. 

Nitrogen and phosphorus can contribute to eutrophication and associated algae blooms. These

blooms can produce negative aesthetic impacts and increase the costs of drinking water

treatment. Turbidity from the blooms can reduce penetration of sunlight in the water column and

thereby limit growth of seagrass beds and other submerged aquatic vegetation, which serve as

critical habitat for fish, crabs, and other aquatic organisms. Decay of algae blooms (as well as

nighttime algal respiration) can depress oxygen levels, leading to fish kills and reduced

biodiversity. Eutrophication is also a factor in blooms of toxic algae and other toxic

microorganisms, such as Pfiesteria piscicida, which can affect human health as well as animal

health. Pathogens and nitrogen in animal waste can also affect human and animal health. 
1-2

Nitrogen in manure is easily transformed into its nitrate form, which can be transported to

drinking water sources and result in potentially fatal health risks to infants. Trace elements in

manure may also present human health and ecological risks. Salts can contribute to salinization

and disruption of ecosystems. Antibiotics, pesticides, and hormones may have low-level, longterm human health and ecological effects.

Ground water sources of drinking water can have impacts from nitrates, pathogens, salts, and

other contaminants from manure. Ground water is typically more prone than surface water to

contamination by nitrates, in particular. In fact, the EPA found that nitrate is the most

widespread agricultural contaminant in drinking water wells and estimates that 4.5 million

people are exposed to elevated nitrate levels from wells (USEPA, 1990).

In soils, salts and trace elements from land-applied manure can accumulate and become toxic to

plants. Salts can deteriorate soil quality by leading to reduced permeability and poor tilth. Crops

may provide a human and animal exposure pathway for trace elements and pathogens.

Air emissions from volatilization occurring at AFOs also produce environmental impacts. Odors

from anaerobic waste decomposition are particularly offensive. Odors can produce mood

disorders such as tension, depression, and fatigue (Schiffman et al., 1995; Thu, 1995). Many

odor-causing substances (e.g., ammonia, hydrogen sulfide, and organic dusts) can also cause

physical effects. Furthermore, volatilized ammonia can be redeposited on the earth and

contribute to eutrophication of surface waters. Methane emissions from anaerobic waste lagoons

are a concern because they increase greenhouse gas concentrations.

Such impacts continue to cause concern despite federal effluent limitation guidelines (ELGs,

“effluent guidelines,” or “guidelines”) that have been in place for feedlots since 1974. 

Essentially, these guidelines apply to large operations and prohibit discharges to surface waters

except when chronic or catastrophic rainfall events cause an overflow from a containment

system. The current regulations do not specifically address discharges that may occur when

wastes are applied to soil.

To help address the various concerns outlined above, the EPA is currently revising the feedlots

effluent limitation guidelines. This report presents the environmental assessment of the proposed

regulations for the pork, poultry, beef, and dairy sectors of concentrated animal feeding

operations (CAFOs). Briefly, each animal sector is composed of:

C pork: facilities that produce mature or immature swine;

C poultry: facilities that produce laying hens, broilers, and turkeys;

C beef: facilities that produce all cattle—this includes veal and replacement

heifers and excludes mature dairy cattle; and

C dairy: facilities that produce mature dairy cattle, whether milked or dry.
1-3

1.2 OVERVIEW OF ANIMAL FEEDING OPERATIONS

Animal production industries have undergone significant changes in the past several decades. 

Domestic and export market forces, technological changes, and industry adaptations have

promoted expansion in the number of confined production units. This includes: 

C growth in both existing and new areas; 

C integration and concentration of some industries; 

C geographic separation of animal production and feed production operations; and 

C the concentration of large quantities of manure and wastewater on farms and in some

watersheds (USDA/USEPA, 1999).

In terms of production, the total number of animal units produced in the U.S. increased by about

4.5 million (approximately three percent) between 1987 and 1992. During the same period,

however, the number of AFOs decreased, indicating a consolidation within the industry overall

and greater production from fewer, larger AFOs (USGAO, 1995b). These changes are not

uniform across animal type or across the country. 

Exhibits 1-1 and 1-2 illustrate the consolidation of animal production between 1978 and 1992. 

The number of operations decreased significantly for most major animal types during this period

(Exhibit 1-1). At the same time, the average number of animals per operation increased

significantly (Exhibit 1-2).
1-4

0

100,000

200,000

300,000

400,000

Cattle Dairy Hogs (top

10

production

states)

Broilers Layers Turkeys

No. of Operations

1978

1992

EXHIBIT 1-1

Industry Consolidation of Animal Feeding Operations

1978 - 1992

Compiled from data in USGAO (1995b).

EXHIBIT 1-2

Increase in the Average Number of 

Animal Units per Operation, 1978-1992

Animal Type

Increase in 

Animal Units/Operation

Swine 134%

Layers 176%

Broilers 148%

Turkeys 129%

Beef Cattle 56%

Dairy Cattle 93%

Derived from data in USGAO (1995b).
1-5

Confined AFOs range in size from small-scale operations with few animals to large, intensive

production facilities. Letson and Gollehon (1996) analyzed 1992 Census of Agriculture data

(USDC/Census Bureau, 1994) to estimate the distribution of confined animals among various

farm sizes (Exhibit 1-3). Their analysis shows that for all animal types, small facilities accounted

for a large share of farms, but a small percentage of animals. Larger farms were less numerous,

but maintained a disproportionately greater percentage of animals. The greatest proportion of

layers and beef cattle were raised on large farms, whereas medium-sized farms accounted for the

greatest proportion of swine, broilers, turkeys, and dairy cattle.

EXHIBIT 1-3

Farms, Number of Head, and Cropland, by Confined Animal Facility Size, 1992

Animal Type

Small

(< 50 AUs)

Medium

(50 to 999 AUs)

Large

(> 1,000 AUs)

Number Percent Number Percent Number Percent

 Swine

Number of farms 115,830 56% 88,042 43% 2,578 1%

Total Head (1,000s) 3,089 5% 38,984 68% 15,270 27%

Total Cropland (1,000 acres) 17,029 30% 37,121 66% 1,795 3%

 Layers

Number of farms 81,903 93% 5,733 6% 599 1%

Total Head (1,000s) 4,033 1% 137,366 39% 209,911 60%

Cropland (1,000 acres) 8,848 90% 881 9% 149 2%

 Broilers

Number of farms 17,657 49% 16,704 47% 1,398 4%

Total Head (1,000s) 2,193 <1% 684,507 73% 246,667 26%

Total Cropland (1,000 acres) 2,207 58% 1,371 36% 211 6%

 Turkeys

Number of farms 7,379 70% 2,911 28% 276 3%

Total Head (1,000s) 892 1% 64,019 74% 21,703 25%

Total Cropland (1,000 acres) 848 60% 535 38% 33 2%

 Beef

Number of farms 134,847 92% 11,411 8% 943 1%

Total Head (1,000s) 995 10% 1,941 19% 7,098 71%

Total Cropland (1,000 acres) 34,199 75% 10,160 22% 1,117 2%

 Dairy

Number of farms 43,700 28% 110,700 71% 939 1%

Total Head (1,000s) 238 3% 8,002 84% 1,252 13%

Total Cropland (1,000 acres) 6,097 16% 32,524 83% 515 1%

Source: Letson and Gollehon (1996).
1-6

The Letson and Gollehon (1996) analysis also provides useful insight regarding the cropland held

by various sizes of AFOs. As shown in Exhibit 1-3, medium and large poultry operations

(particularly layer facilities and beef operations) account for a large percentage of animals, but a

small percentage of cropland on which to apply manure. Pork and dairy operations exhibit a

similar characteristic for large farms. The amount of cropland ultimately influences animal waste

disposal options. Historically, farm enterprises integrated crop and animal production by using

the manure generated to fertilize crops, constituting a crucial element of manure management. 

Such integrated pork and dairy operations are still common, particularly in the eastern Corn Belt. 

However, the breeding and raising phases of livestock production increasingly occurs in largescale, specialized operations. This trend toward high-volume commercial enterprises separates

the locations of manure generation and cropland available for its application (Letson and

Gollehon, 1996).

1.3 ORGANIZATION OF REPORT

This report presents a water-quality-based environmental impact assessment of the proposed

regulations for swine, poultry, beef, and dairy CAFOs. Chapter 2 quantifies the amount of

manure and total solids generated by swine, poultry, beef, and dairy operations as well as by

other livestock and humans. Chapter 2 also provides information on animal manure constituents. 

Chapter 3 describes the potential human health and ecological hazards from manure pollutants. 

Chapter 4 discusses studies that estimate the potential environmental impact of animal waste at

the national level and describes other reported impacts. Finally, Chapter 5 describes potential

and reported benefits from the implementation of proposed management practices to control

wastes from animal feeding operations.

To present a sense of the scope of the problem, this report relies on state and federal information,

as well as news articles and data collected by environmental advocacy groups. While data from

government agencies are considered more reliable, the resources are not available to thoroughly

track CAFO-related releases of pollutants to the environment and the resulting environmental

and human health impacts. This more inclusive approach is intended to provide a sense of the

possible scope of the impacts until state and federal agencies can fully document them.
2-1

2. ANIMAL WASTE CHARACTERISTICS AND TRANSPORT

TO SURFACE WATERS

Animal feeding operations generate large volumes of waste of the following types:

C animal manure and urine;

C hair, feathers, and corpses;

C bedding and spilled feed;

C wash-flush water; and

C other processing wastes.

Many of these wastes are convertible to useful resources, such as fertilizer, soil conditioner, and

feed (Shih, 1993; Edwards and Daniel, 1992a; USDA, 1992). However, these wastes can be a

source of environmental degradation when improperly managed. In many cases, manure is

applied in excess of crop nutrient requirements, due to manure nutrient ratios that differ from

crop needs and/or lack of available nearby land. For example, the U.S. Fish and Wildlife Service

estimates that the amount of phosphorus currently excreted by livestock in Nebraska exceeds

what can currently be applied to farm fields at agronomic rates statewide (USFWS, 2000). This

problem has received increasing attention as livestock operations have become more

concentrated, with a trend toward more animals on fewer farms and less land. Incidents of

discharges from waste storage lagoons, excessive runoff, leaking lagoons, and offensive odors

have heightened public awareness and concerns about environmental impacts from AFOs.

Although many of the above-mentioned wastes can pose environmental risks, this chapter

focuses on the characteristics of manure, which is often cited as a significant contributor to water

quality degradation (USEPA, 1997a). In general, pollutant production figures reported here are

based on 1997 data, the most readily available Census of Agriculture data (USDA/NRCS, 2000;

USDA/NASS, 1999). USDA’s Natural Resources Conservation Service (NRCS) estimated the

quantities of manure and primary nutrients generated by livestock. NRCS based its approach on

Lander et al. (1998), which provides a more detailed description of the methods and data sources

used.

2.1 QUANTITY OF MANURE GENERATED

2.1.1 Total Manure

The large quantity of animal waste helps demonstrate why proper handling and disposal are

essential in limiting environmental risks from manure. Animal manure is significantly more

abundant than human waste. USDA’s National Resources Conservation Service estimated that

291 billion pounds of manure measured on a wet basis (132 million metric tons when dried) was

generated in 1997 from swine, poultry, and beef and dairy cattle (USDA/NRCS 2000) (see 
2

These quantities reflect the most recent estimates by USDA of manure generation from livestock

operations, using data from the 1997 Census of Agriculture (USDA/NASS, 1999) and an approach developed by

Lander et al. (1998). USDA’s estimates are calculated on a wet manure basis, but expressed on a “dry-state” basis

(to adjust for water content). Previous studies have reported a wide range of manure generation estimates for

livestock and poultry operations that vary depending on the approach used and on whether the load is estimated on a

wet or dry basis.

2-2

Exhibit 2-1).2 By comparison, the human sanitary waste production for that year was only 49

billion pounds (22 million metric tons total solids, dry-weight basis) (USDA/NRCS, 1996). This

comparison, however, cannot be used as a surrogate for the relative extent of environmental

impacts, since human and animal wastes are handled differently. For example, human sanitary

waste is typically treated at a wastewater treatment plant, with the liquid effluent being

discharged after treatment to surface water and the residual solids (sludge, or biosolids) being

land applied, landfilled, or incinerated. Animal waste is typically land applied in its entirety,

without an associated point source discharge (if properly applied). Nevertheless, the figures

provide a sense of the significance of the total animal waste problem, especially in light of

industry trends toward increased concentration of animals on farms. The figures are also relevant

when considering that disposal of human waste is highly regulated, but disposal of animal waste

has been largely unregulated.

EXHIBIT 2-1

Manure Production by Both Livestock and Humans

Species

Average

Mass of Species

(pounds)

Pounds Per 1,000 Pounds Live Unit Weight Per Day

Wet-Weight Manure a Dry-Weight Manure b

Swine 135 84 8.2

Layer 4.0 64 16

Broiler 2.0 85 21

Turkey 15 47 12

Beef 800 58 6.9

Dairy 1,400 86 10

Human 150 30 3.3

Sources: Livestock data are “as excreted” and are from ASAE (1999); human waste data are “as excreted” and are

from USDA/NRCS (1996).

Values rounded to two significant figures.

a

 Includes feces and urine as voided.

b

 Calculated using average solids content for each category, based on data from USDA/NRCS (1996).

2.1.2 Recoverable Manure

Although the above figures give a good indication of the magnitude of the total animal waste

problem, they are not the best indicators of the problem that the proposed regulations address,

because much of the total manure is generated by grazing or pastured animals, which are not the

subject of the proposed regulations. Instead, the regulations address the manure generated by

confined animal facilities, which is considered recoverable manure because waste is contained

within the production area. Recoverable manure may include scraped manure, stored slurry
2-3

manure, lagoon effluent, and poultry litters, and may be applied later to croplands as fertilizer

(Westerman et al., 1985).

It is important to estimate the amount of recoverable manure produced, not only to provide a

good representation of the amount produced by confined animal operations, but also because

recoverable manure may be a usable resource. For each state, Exhibit 2-2 lists the fraction of

manure produced by major animal sectors that is recoverable. Lander et al. (1998) prepared these

estimates using state survey responses from a study by Van Dyne and Gilbertson (1978).

As presented in Exhibit 2-2, nearly all manure (90 to 100 percent) from layers and broilers in the

major producing states was recoverable. Turkey manure recovery ratios varied more widely in

the top producing states. For example, recovery ratios ranged from 70 to 100 percent in North

Carolina, South Carolina, Texas, Virginia, and Wisconsin, whereas they were only 20 to 45

percent in California, Michigan, and Minnesota. Approximately 90 percent of all swine manure

in North Carolina was recoverable. In other major pork producing states, manure recovery ratios

ranged from 65 to 85 percent. In top producing beef states, only five to ten percent of the manure

from grazing cattle was recoverable, whereas 60 to 90 percent of the manure from fattened cattle

was recoverable. Recovery ratios for milk cows in top producing states ranged from 75 to 90

percent.
EXHIBIT 2-2

Fraction of Recoverable Manure, by Animal and by State (Top Ten Producing States Indicated b

State Beef (Grazing) Beef (Fattened) Milk Swine (Breeding) Swine (Other) Laying Hen/Pullet Pullets (<3 mos.) Broilers Tu

(slau

AL 0.10 0.70 0.40 0.75 0.75 0.95 0.95 0.98 AZ 0.05 0.85 0.80 0.85 0.85 0.90 0.90 0.90 

AR 0.10 0.50 0.50 0.50 0.50 0.80 0.80 0.95 

CA 0.05 0.85 0.80 0.85 0.85 1.00 1.00 1.00 

CO 0.05 0.85 0.80 0.85 0.85 0.95 0.95 0.95 

CT 0.10 0.85 0.90 0.80 0.80 1.00 1.00 0.95 DE 0.10 0.85 0.80 0.80 0.80 0.90 0.90 0.95 

FL 0.00 0.00 0.50 0.40 0.40 0.95 0.95 0.95 

GA 0.00 0.75 0.70 0.50 0.50 0.90 0.90 0.95 

ID 0.00 0.85 0.95 0.70 0.70 0.90 0.90 0.90 

IL 0.10 0.60 0.80 0.70 0.70 1.00 1.00 1.00 

IN 0.10 0.75 0.60 0.80 0.80 0.95 0.95 0.95 IA 0.10 0.63 0.87 0.80 0.80 0.99 0.99 0.99 

KS 0.05 0.75 0.85 0.80 0.80 0.95 0.95 0.95 

KY 0.08 0.70 0.70 0.60 0.60 0.80 0.80 0.80 

LA 0.00 0.80 0.50 0.80 0.80 1.00 1.00 1.00 

ME 0.10 0.85 0.80 0.80 0.80 0.90 0.90 0.95 

MD 0.10 0.85 0.80 0.80 0.80 0.90 0.90 0.95 

MA 0.10 0.85 0.80 0.80 0.80 0.90 0.90 0.95 

MI 0.08 0.75 0.90 0.66 0.66 1.00 1.00 1.00 

MN 0.15 0.90 0.90 0.85 0.85 1.00 1.00 1.00 

MS 0.10 0.75 0.60 0.65 0.65 0.90 0.90 0.95 

MO 0.10 0.60 0.65 0.65 0.65 0.85 0.85 0.90 

MT 0.01 0.85 0.75 0.80 0.80 1.00 1.00 1.00 

NE 0.08 0.90 0.80 0.66 0.66 1.00 1.00 1.00 
EXHIBIT 2-2

Fraction of Recoverable Manure, by Animal and by State (Top Ten Producing States Indicated b

State Beef (Grazing) Beef (Fattened) Milk Swine (Breeding) Swine (Other) Laying Hen/Pullet Pullets (<3 mos.) Broilers Tu

(slau

NV 0.05 0.85 0.80 0.85 0.85 0.90 0.90 0.90 

NH 0.10 0.85 0.80 0.80 0.80 1.00 1.00 1.00 

NJ 0.10 0.85 0.80 0.80 0.80 0.90 0.90 0.95 

NM 0.00 0.80 0.85 0.85 0.90 0.90 0.90 0.90 

NY 0.10 0.85 0.80 0.80 0.80 0.90 0.90 0.95 NC 0.00 0.75 0.59 0.90 0.90 1.00 1.00 1.00 ND 0.00 0.85 0.80 0.50 0.50 1.00 1.00 1.00 

OH 0.10 0.70 0.90 0.75 0.75 1.00 1.00 1.00 

OK 0.10 0.80 0.65 0.75 0.75 1.00 1.00 1.00 

OR 0.05 0.85 0.60 0.85 0.85 0.90 0.90 0.90 

PA 0.05 0.85 0.80 0.80 0.80 0.95 0.95 0.95 

RI 0.10 0.85 0.80 0.80 0.80 0.90 0.90 0.95 

SC 0.00 0.80 0.59 0.49 0.49 1.00 1.00 1.00 

SD 0.10 0.75 0.80 0.70 0.70 0.95 0.95 0.95 

TN 0.10 0.75 0.60 0.65 0.65 0.90 0.90 0.95 TX 0.05 0.85 0.75 1.00 1.00 1.00 1.00 1.00 UT 0.05 0.85 0.80 0.85 0.85 0.90 0.90 0.90 VT 0.20 0.90 0.90 0.80 0.80 0.90 0.90 0.95 

VA 0.10 0.85 0.60 0.80 0.80 1.00 1.00 1.00 

WA 0.05 0.85 0.80 0.85 0.85 0.80 0.80 0.80 WV 0.00 1.00 0.80 0.75 0.75 1.00 1.00 1.00 

WI 0.08 0.70 0.90 0.66 0.66 1.00 1.00 1.00 

WY 0.05 0.80 0.80 0.75 0.75 0.95 0.95 0.95 

Source: Recoverable fractions are from Lander et al. (1998). Top producing states were identified through the 1992 Census of Agriculture(USDC/Census Bureau, 1994).
2-6

Exhibit 2-3 lists the amount of recoverable manure and recoverable nutrients (nitrogen and

phosphorus) generated by individual animal sectors (beef, dairy, swine, and poultry operations)

throughout the U.S. in 1997. Nationwide, approximately 16 percent of beef manure was

recoverable, accounting for 22 percent of total recoverable livestock manure (dry-state). 

Approximately 76 percent of dairy manure was recoverable, translating to 37 percent of

recoverable livestock manure. About 92 percent of swine manure was recoverable, accounting

for 13 percent of total recoverable livestock manure. Nationwide, 98 percent of poultry manure

was recoverable, representing approximately 27 percent of recoverable livestock manure. These

quantities reflect the most recent estimates by USDA of manure generation from livestock and

poultry operations, using an approach developed by Lander et al. (1998). The benefits analysis

contains additional information on manure production.

EXHIBIT 2-3

Estimated Recoverable Manure and Manure Nutrients Generated by Sector

Animal Group

1997 Manure Production

Recoverable

Manure 

(million lbs)

Percent of Total

Manure Production

That Is Recoverable

Recoverable

Nitrogen 

(1,000 lbs)

Recoverable

Phosphorus

(1,000 lbs)

Beef 28,637 16% 484 340

Dairy 47,476 76% 672 266

Swine 17,120 92% 274 277

Poultry - Total 34,979 98% 1,153 554

Layers 7,101 98% 231 123

Broilers 19,199 98% 616 255

Turkeys 8,679 98% 306 175

Total, all livestock 128,212 44% 2,583 1,437

Calculated by USDA/NRCS based on 1997 Census of Agriculture (USDA/NASS, 1999) using procedures in

Lander et al. 1998. Numbers are “dry state” (wet basis, adjusted for water content).

Recoverable Nitrogen

Poultry manure has the highest amount of recoverable nitrogen (58 percent), making up 45

percent of all recoverable nitrogen for the sectors under consideration. Dairy manure has the

next highest amount of recoverable nitrogen (30 percent), accounting for 26 percent of all

recoverable nitrogen for the sectors under consideration. Manure from pork operations had the

third highest amount of recoverable nitrogen (23 percent), accounting for 11 percent of the total

for these sectors. Beef manure had the lowest ratio of recoverable nitrogen (6 percent), but due

to volume this source accounted for 19 percent of the total for all sectors (Lander et al., 1998).

Recoverable Phosphorus

Poultry manure also had the highest amount of recoverable phosphorus (83 percent), making up

39 percent of all recoverable phosphorus. Swine manure had the second highest amount of

recoverable phosphorus (78 percent), accounting for 19 percent of the recoverable phosphorus
3

Ammonia is also a nutrient but is listed separately here because it exhibits additional environmental

effects, such as aquatic toxicity and direct dissolved oxygen demand.

4

Total Kjeldahl nitrogen is the sum of organic nitrogen in the trinegative oxidation state and ammonia.

2-7

from the sectors considered. Manure from dairy operations ranked third for recoverable

phosphorus (66 percent) and generated 19 percent of the recoverable phosphorus from all four

sectors. As with nitrogen, beef manure also had the lowest ratio of recoverable phosphorus (14

percent), but due to volume this source ranked second for all sectors with 24 percent (Lander et

al., 1998).

2.2 POLLUTANTS OF CONCERN

The primary pollutants associated with animal waste are nutrients (particularly nitrogen and

phosphorus), ammonia,3 pathogens, and organic matter. Animal waste is also a source of salts

and trace elements, and to a lesser extent, antibiotics, pesticides, and hormones. The actual

composition of manure depends on the animal species, size, maturity, and health, as well as on

the composition (e.g., protein content) of animal feed (Phillips et al., 1992). After waste has

been excreted, it may be altered further by the bedding and waste feed, and may be diluted with

water (Loehr, 1972; USDA, 1992). 

The following sections describe the characteristics of each main group of AFO pollutants. The

estimates of manure pollutant production are based on average values reported in the scientific

literature and compiled by the American Society of Agricultural Engineers (ASAE, 1999),

USDA/NRCS (1996), and USDA/ARS (1998).

2.2.1 Nutrients

The three primary nutrients in manure are nitrogen, phosphorus, and potassium. Much of the

past research on animal manure has focused on these constituents, given their importance as

cropland fertilizers. The following discussions provide more detail on nitrogen and phosphorus

characteristics and concentrations in manure. Scientific literature and policy statements

commonly cite these two nutrients as key sources of water quality impairments. In the central

United States, a 1995 estimate notes that 37 percent of all nitrogen and 65 percent of all

phosphorus inputs to watersheds come from manure (USFWS, 2000). Actual or anticipated

levels of potassium in ground water and surface water are unlikely to pose hazards to human

health or aquatic life (Wetzel, 1983). Potassium does contribute to salinity, however, and

applications of high salinity manure are likely to decrease the fertility of the soil.

Exhibit 2-4 presents the amounts of total Kjeldahl nitrogen,4

 total phosphorus, orthophosphorus,

and potassium generated per 1,000 pounds live animal weight per day (ASAE, 1999). For

comparison, Exhibit 2-4 presents similar information for humans. The figures illustrate that perpound nutrient output varies among animal types and is much higher for animals than humans.
5

In an anaerobic lagoon, the organic fraction is about 20 to 30 percent of total nitrogen (USDA, 1992).

2-8

EXHIBIT 2-4

Primary Nutrients in Both Livestock and Human Manures

Nutrient

Animal Group

Human Swine Layer Broiler Turkey Beef Dairy

Mass of animal (lbs.) 135 4.0 2.0 15 800 1,400 150

Pounds per 1,000 pounds live animal weight per day

Nitrogen 

(Total Kjeldahl)

0.52 0.84 1.1 0.62 0.34 0.45 0.20

Phosphorus (Total) 0.18 0.30 0.30 0.23 0.092 0.094 0.02

Orthophosphorus 0.12 0.09 n/a n/a 0.03 0.061 n/a

Potassium 0.29 0.30 0.40 0.24 0.21 0.29 0.07

Sources: Livestock data are “as excreted” and are from ASAE (1999); human waste data are “as excreted” and are

from USDA/NRCS (1996).

Values rounded to two significant figures.

n/a = not available

Nitrogen Compounds

Nitrogen (N) is an essential nutrient required by all living organisms. Nitrogen occurs in the

environment in gaseous forms (elemental nitrogen, N2; nitrogen oxide compounds, N2O and NOx;

and ammonia, NH3); water soluble forms (ammonia, NH3; ammonium, NH4

+

; nitrite, NO2

-

; and

nitrate, NO3

-

); and as organic nitrogen, bound up in the proteins of living organisms and decaying

organic matter (Brady, 1990). The transformation of the different forms of nitrogen among land,

water, air, and living organisms is known as the nitrogen cycle (Exhibit 2-5).

Nitrogen in fresh manure exists primarily in the organic and ammonium forms (NCAES, 1982). 

Sixty to 90 percent of total nitrogen in fresh manure is in the organic form.5

 Organic nitrogen in

the solid content of animal feces is mostly in the form of complex molecules associated with

digested food, while organic nitrogen in urine is mostly in the form of urea ((NH2)2CO) (USDA,

1992). In organic form, nitrogen is unavailable to plants. However, via microbial processes,

organic nitrogen is transformed to ammonium (NH4

+

) and nitrate (NO3

-

) forms, which are

bioavailable and therefore have fertilizer value.

Under aerobic conditions, ammonia can oxidize to nitrites and nitrates. Subsequent anaerobic

conditions can result in denitrification (transformation of nitrates/nitrites to gaseous nitrogen

forms). Overall, depending on the animal type and specific waste management practices,

between 30 and 90 percent of nitrogen excreted in manure can be lost before use as a fertilizer

(Vanderholm, 1975).
EXHIBIT 2-5

The Nitrogen Cycle
2-10

Phosphorus Compounds

Phosphorus exists in solid and dissolved phases, in both organic and inorganic forms. Like

nitrogen, the various forms of phosphorus are subject to transformation (Exhibit 2-6). Dissolved

phosphorus in the soil environment consists of orthophosphates (PO4

-3, HPO4-2, or H2PO4-

),

inorganic polyphosphates, and organic phosphorus (Poultry Water Quality Consortium, 1998). 

Solid phosphorus exists as organic phosphorus in dead and living materials; mineral phosphorus

in soil components; adsorbed phosphorus on soil particles; and precipitate phosphorus, which

forms upon reaction with soil cations such as iron, aluminum, and calcium (Poultry Water

Quality Consortium, 1998). Orthophosphate species, both soluble and attached, are the

predominant forms of phosphorus in the natural environment (Bodek et al., 1988). Soluble

(available or dissolved) phosphorus generally accounts for a small percentage of total soil

phosphorus. However, soils saturated with phosphorus can have significant occurrences of

phosphorus leaching. Soluble phosphorus is the form used by plants and is subject to leaching. 

About 73 percent of the phosphorus in most types of fresh livestock waste is in the organic form

(USDA, 1992). As animal waste ages, the organic phosphorus mineralizes to inorganic

phosphate compounds and becomes available to plants.

2.2.2 Ammonia

Ammonium (NH4

+

) is produced when microorganisms break down organic nitrogen products

(e.g., urea and proteins in manure). This decomposition can occur in either aerobic or anaerobic

environments. In solution, ammonium enters into an equilibrium reaction with ammonia (NH3),

as shown in the following equation:

NH4

+ W NH3 + H+

Up to 50 percent or more of the nitrogen in fresh manure may be in the ammonia form or

converted to ammonia relatively quickly once manure is excreted (Vanderholm, 1975). 

Ammonia is very volatile, and much of it is emitted as a gas, although it may also be absorbed by

or react with other substances.

Higher pH levels (lower H+

 concentrations) favor the formation of ammonia, while lower pH

levels (higher H+

 concentrations) favor the formation of ammonium. The ammonia form is

subject to volatilization. 

The ammonia content of fresh manure varies among animal species and changes as the manure

ages. Ammonia content may increase as organic matter breaks down; it may decrease when

volatilization occurs or when nitrate oxidizes to nitrite under aerobic conditions.
EXHIBIT 2-6

The Phosphorus Cycle
2-12

2.2.3 Pathogens

Both manure and animal carcasses can be sources of pathogens (disease-causing organisms) in

the environment (Juranek, 1995). Livestock manure may contain bacteria, viruses, fungi,

helminths, protozoa, and parasites, many of which are pathogenic (USDA, 1998; Jackson et al.,

1987). For example, researchers have isolated pathogenic bacteria and viruses from feedlot

wastes (Derbyshire et al., 1966; Hrubant, 1973; Derbyshire and Brown, 1978). In addition,

USFWS (2000) has shown fields receiving animal waste applications to have elevated levels of

fecal coliforms and fecal streptococci. Specifically, bacteria such as Escherichia coli O157:H7,

Salmonella species, Campylobacter jejuni, Listeria monocytogenes, and Leptospira species are

often found in livestock manure and have also been associated with waterborne disease. A recent

study by the USDA revealed that about half the beef cattle presented for slaughter during July

and August 1999 carried Escherichia coli O157:H7 (Elder et al., 2000). Also, protozoa,

including Cryptosporidium parvum and Giardia species (such as Giardia lamblia), may occur in

animal waste. Cryptosporidium parvum is associated with cows in particular; newborn dairy

calves are especially vulnerable to infection and excrete large numbers of the infectious oocysts

(USDA, 1998). Most pathogens are shed from host animals with active infections.

Presence of bacteria (and other pathogens) is often measured by the level of fecal coliforms,

Escherichia coli, or enterococci in manure (Bouzaher et al., 1993). Use of indicator organisms

such as these has limitations; specifically, that there are no established relationships between

fecal coliform and pathogen contamination. However, indicators are still used because specific

pathogen testing protocols are too time consuming, expensive, and/or insensitive to be used for

monitoring purposes (Shelton, 2000). Exhibit 2-7 lists the number of total coliform bacteria,

fecal coliform bacteria, and fecal streptococcus bacteria per cubic foot of manure for swine,

poultry, beef, and dairy animals (ASAE, 1999).

EXHIBIT 2-7

Coliform Bacteria in Manure (colonies per cubic foot of manure, as excreted)

Animal Group Total Coliform

Bacteria

Fecal Coliform

Bacteria

Fecal Streptococcus

Bacteria

Swine 1.6 x 1011 5.9 x 1010 18 x 1011

Poultry (layers) 4.7 x 1011 3.2 x 1010 0.69 x 1011

Beef 3.2 x 1011 14 x 1010 1.5 x 1011

Dairy 36 x 1011 5.2 x 1010 3.0 x 1011

Source: ASAE (1999).

Values rounded to two significant figures.

2.2.4 Organic Matter

Livestock manures contain many carbon-based, biodegradable compounds. These compounds

are of concern in surface water because dissolved oxygen is consumed as aquatic bacteria and

other microorganisms decompose these compounds. This process reduces the amount of oxygen

available for aquatic animals.
2-13

The greater the manure’s concentration of materials that can be readily decomposed, the greater

the manure’s oxygen demand. Two measures are often used to estimate oxygen demand. 

Biochemical oxygen demand (BOD) is an indirect measure of the concentration of biodegradable

substances present in an aqueous solution. The ultimate BOD is the amount of oxygen required

to completely degrade the waste biologically under aerobic conditions. BOD is often expressed

as BOD5. This measure refers to the amount of oxygen required by bacteria while decomposing

organic matter under aerobic conditions over a five-day period at 20EC in a laboratory test. 

BOD5 is expressed as the number of milligrams of oxygen required to support oxidation of the

compounds in one liter of liquid waste. Alternatively, the chemical oxygen demand (COD) test

uses a chemical oxidant. This test provides an approximation of the ultimate BOD and can be

estimated more quickly than the five days required for the BOD5 test. If the waste contains only

readily available organic bacterial food and no toxic matter, the COD values correlate with BOD

values obtained from the same wastes (Dunne and Leopold, 1978).

Exhibit 2-8 lists BOD5 and COD estimates for manure generated by swine, poultry, beef, and

dairy animals and, for comparison, provides values for domestic sewage. Reported BOD5 values

for various untreated animal manures range from 24,000 mg/L to 33,000 mg/L. COD values

range from 25,000 mg/L to 260,000 mg/L. Dairy and beef cattle manure have BOD5 and COD

values of similar magnitude. By comparison, the BOD5 value for raw domestic sewage ranges

from 100 mg/L to 300 mg/L. Even after biological treatment in anaerobic lagoons, animal waste

BOD5 concentrations (200 mg/L to 3,800 mg/L) are much higher than those of municipal

wastewater treated to the secondary level (about 20 mg/L) (USDA, 1992).
2-14

EXHIBIT 2-8

Reported BOD5 and COD Concentrations for Manures and Domestic Sewage

Waste BOD5

(mg/L)

COD

(mg/L)

Swine manure

Untreated

Anaerobic lagoon influent

Anaerobic lagoon effluent

27,000 to 33,000

13,000

300 to 3,600

25,000 to 180,000

n/a

n/a

Poultry manure

Untreated (chicken)

Anaerobic lagoon influent (poultry)

Anaerobic lagoon effluent (poultry)

24,000

9,800

600 to 3,800

100,000 to 260,000

n/a

n/a

Dairy cattle manure

Untreated

Anaerobic lagoon influent

Anaerobic lagoon effluent

26,000

6,000

200 to 1,200

68,000 to 170,000

n/a

n/a

Beef cattle manure

Untreated

Anaerobic lagoon influent

Anaerobic lagoon effluent

28,000

6,700

200 to 2,500

73,000 to 260,000

n/a

n/a

Domestic sewage

Untreated

After secondary treatment

100 to 300

20

400 to 600

n/a

Sources: Untreated values, except for beef manure BOD5, are from NCAES (1982). The BOD5 value for beef manure

is from ASAE (1997). Lagoon influent and effluent concentrations are from USDA/NRCS (1996).

Values rounded to two significant figures.

n/a = not available

2.2.5 Salts and Trace Elements

The salinity of animal manure is directly related to the presence of the nutrient potassium and

dissolved mineral salts that pass through the animal. In particular, significant concentrations of

soluble salts containing the cations sodium and potassium remain from undigested feed that

passes unabsorbed through animals (NCAES, 1982). Other major cations contributing to salinity

are calcium and magnesium; the major anions are chloride, sulfate, bicarbonate, carbonate, and

nitrate (National Research Council, 1993). Salinity tends to increase as the volume of manure

decreases during decomposition and evaporation (Gresham et al., 1990).

Trace elements in manure that are of environmental concern include arsenic, copper, selenium,

zinc, cadmium, molybdenum, nickel, lead, iron, manganese, aluminum, and boron. Arsenic,

copper, selenium, and zinc are often added to animal feed as growth stimulants or biocides

(Sims, 1995). Trace elements may also end up in manure through use of pesticides, which

farmers apply to livestock to suppress houseflies and other pests (USDA/ARS, 1998).

It is useful to compare trace element concentrations in manure to those in municipal sewage

sludge, which is regulated by the EPA’s Standards for the Use or Disposal of Sewage Sludge

promulgated under the Clean Water Act and published in 40 CFR Part 503 (USEPA, 1993c). 

Regulated trace elements in sewage sludge include arsenic, cadmium, chromium, copper, lead,
2-15

mercury, molybdenum, nickel, selenium, and zinc. Sims (1995) has reported total concentrations

of trace elements in animal manures as comparable to those in some municipal sludges, with

typical values well below the maximum concentrations allowed by Part 503 for land-applied

sewage sludge.

2.2.6 Antibiotics

A number of pharmacological agents, including antibiotics, are used in animal feeding operations

and can appear in animal wastes. Some of these agents are used only therapeutically (e.g., to

treat illness). Others are used both therapeutically and as feed additives to promote growth or to

improve feed conversion efficiency. In 1991, farmers used an estimated 19 million pounds of

antibiotics for disease prevention and growth promotion in animals. From 60 to 80 percent of

animals receive antibiotics during their productive life span (Tetra Tech, 2000a). Use as feed

additives accounts for most of the mass of antibiotics used in both the swine and poultry

industries and accounts for the presence of antibiotics in the resulting manure. Although

antibiotic residues in beef and dairy manure are also a concern, the EPA could not locate any

literature on levels of antibiotics in manure. Estimated concentrations of the antibiotic

chlortetracycline in the lagoon systems of a pork producer in Nebraska range from 150 to 300

mg/L; that producer currently uses 16 different antibiotics as feed and drinking water additives

(USFWS, 2000).

2.2.7 Hormones

Hormones are the chemical messengers that carry instructions to target cells throughout the body

and are normally produced by the body’s endocrine glands. The target cells read and follow the

hormones’ instructions, sometimes building a protein or releasing another hormone. These

actions lead to many bodily responses such as a faster heart beat or bone growth. Hormones

include steroids (estrogen, progesterone, testosterone), peptides (antidiuretic hormone),

polypeptides (insulin), amino acid derivatives (melatonin), and proteins (prolactin, growth

hormone). Natural hormones are potent; only very small amounts are needed to cause an effect. 

Specific hormones are administered to cattle to increase productivity in the beef and dairy

industries, and several studies have shown that hormones are present in animal manures (Mulla,

1999). For example, poultry manure has been shown to contain about 30 ng/g of estrogen, and

about the same levels of testosterone (Shore et al., 1995). Also, estrogen was found in

concentrations up to 20 ng/L in runoff from fields fertilized with chicken manure (Shore et al.,

1995).

2.2.8 Other Pollutants of Concern

AFOs can also be a source of gas emissions, particulates, and pesticides. A general overview of

each group of pollutants follows:

C Gas emissions. The degradation of animal wastes by microorganisms produces a

variety of gases. Sources of odor include animal confinement buildings, waste

lagoons, and land application sites. In addition to ammonia, which was discussed
2-16

earlier, three main gases generated from manure are carbon dioxide, methane, and

hydrogen sulfide. Aerobic conditions yield mainly carbon dioxide, while anaerobic

conditions generate both methane and carbon dioxide. Anaerobic conditions, which

dominate in typical, unaerated animal waste lagoons, also generate hydrogen sulfide

and over 150 other odorous compounds, including volatile fatty acids, phenols,

mercaptans, aromatics, sulfides, and various esters, carbonyls, and amines (O’Neill

and Phillips, 1992; USDA, 1992; Bouzaher et al., 1993).

C Particulates. Sources of particulate emissions from AFOs may include dried manure,

feed, epithelial cells, hair, and feathers. The airborne particles make up an organic

dust, which includes endotoxin (the toxic protoplasm liberated when a microorganism

dies and disintegrates), adsorbed gases, and possibly steroids. At least 50 percent of

dust emissions from swine operations may be respirable (Thu, 1995).

C Pesticides. Pesticides are used in animal feeding operations and can appear in animal

wastes. Farmers may use pesticides on crops grown for animal consumption or

directly in animal housing areas to control parasites (among other reasons). However,

little information is available regarding the concentrations of pesticides in animal

wastes or on their bioavailability in waste-amended soils.

2.3 TRANSPORT OF MANURE POLLUTANTS TO SURFACE WATER

Pollutants found in animal manures can reach surface water by several mechanisms. These can

be categorized as either surface discharges or other discharges. Surface discharges can result

from runoff, erosion, spills, and dry-weather discharges. In surface discharges, the pollutant

travels overland or through drain tiles with surface inlets to a nearby stream, river, or lake. 

Direct contact between confined animals and surface waters is another means of surface

discharge. For other types of discharges, the pollutant travels via another environmental medium

(ground water or air) to surface water. 

2.3.1 Surface Discharges

Runoff

Feedlot runoff contains extremely large loads of nutrients and oxygen-demanding substances,

which can severely degrade surface water quality (Mulla, 1999). Water that falls on man-made

surfaces or soil and fails to be absorbed will flow across the surface. This process is called

runoff. Surface discharges of manure pollutants can originate from feedlots and from overland

runoff at land application sites. Runoff is especially likely at open-air feedlots, when rainfall

occurs soon after application, and when farmers over-apply or misapply manure. For example,

experiments show that for all animal wastes, the application rate has a significant effect on the

runoff concentration (Daniel et al., 1995). Other factors that promote runoff to surface waters are

steep land slope, high rainfall, low soil porosity or permeability, and close proximity to surface

waters. In addition, manure applied to saturated or frozen soils is more likely to run off the soil

surface (Mulla, 1999). Runoff of pollutants dissolved into rainwater is a significant transport
2-17

mechanism for water soluble pollutants, including nitrate, nitrite, and organic forms of

phosphorus.

Runoff of manure pollutants has been identified as a factor in a number of documented impacts

from AFOs. For example, in 1994, an environmental advocacy group noted multiple runoff

problems for a swine operation in Minnesota (Clean Water Action Alliance, 1998), and in 1996,

the State of Ohio identified runoff from manure spread on land at several Ohio operations that

were feeding swine and chicken (Ohio Department of Natural Resources, 1997). More

discussion of runoff and its impacts on the environment and human health appears later in this

document.

Erosion 

In addition to runoff, surface discharges can occur by erosion, in which the soil surface is worn

away by the action of water or wind. Erosion is a significant transport mechanism for landapplied pollutants, such as phosphorus, that are strongly sorbed to soils (Gerritse, 1977). 

The USDA Natural Resources Conservation Service (NRCS) reviewed the manure production in

a watershed in South Carolina. Agricultural activities in the project area are a major influence on

the streams and ponds in the watershed and contribute to nutrient-related water quality problems

in the headwaters of Lake Murray. NRCS found that bacteria, nutrients, and sediment from soil

erosion are the primary contaminants affecting the waters in this watershed. The NRCS has

calculated that soil erosion, occurring on over 13,000 acres of cropland in the watershed, ranges

from 9.6 to 41.5 tons per acre per year (USEPA, 1997b).

Spills and Dry-Weather Discharges

Surface discharges can occur through spills or other discharges from lagoons. Catastrophic spills

from large manure storage facilities can occur primarily through overflow following large storms

or by intentional releases (Mulla et al., 1999). Other causes of spills include pump failures,

malfunctions of manure irrigation guns, and breakage of pipes or retaining walls. Manure

entering tile drains has a direct route to surface water. (Tile drains are a network of pipes buried

in fields below the root zone of plants to remove subsurface drainage water from the root zone to

a stream, drainage ditch, or evaporation pond.) In addition, spills can occur as a result of

washouts from floodwaters when lagoons are sited on floodplains. There are also indications

that discharges from siphoning lagoons occur deliberately as a means to reduce the volume in

overfull lagoons (Clean Water Action Alliance, 1998). An independent review of Indiana

Department of Environmental Management records indicated that two common causes of waste

releases in that state were intentional discharges and accidental discharges resulting from lack of

operator knowledge (Hoosier Environmental Council, 1997).

Localities have identified numerous such discharges. The Ohio Department of Natural

Resources (ODNR) documented chicken manure traveling through tile drains into a nearby

stream in several instances occurring in 1994, 1995, and 1996 (ODNR, 1997). In 1995, a

discharge of 25 million gallons of manure from swine farms in North Carolina was documented

(Meadows, 1995; NRDC, 1995; Warrick, 1995b). Subsequent discharges of hundreds of
2-18

thousands of gallons of manure were documented from swine operations in Iowa (1996), Illinois

(1997), and Minnesota (1997) (IDNR, 1998; Illinois Stewardship Alliance, 1997; Macomb

Journal, 1999; Clean Water Action Alliance, 1998). Between 1994 and 1996, half a dozen

discharges from poultry operations in Ohio resulted when manure entered drain tiles (ODNR,

1997). In 1996, more than 40 animal waste spills occurred in Iowa, Minnesota, and Missouri

alone (U.S. Senate, 1997). In 1998, a dairy feedlot in Minnesota discharged 125,000 gallons of

manure (Clean Water Action Alliance, 1998). Acute discharges of this kind frequently result in

dramatic fish kills. For example, fish kills were reported as a result of the North Carolina, Iowa,

Minnesota, and Missouri discharges mentioned above.

Direct Contact between Confined Animals and Surface Water

Finally, surface discharges can occur as a result of direct contact between confined animals and

the rivers or ponds that are located within their reach. Historically, people located their farms

near waterways for both water access by animals and discharge of wastes. Certain animals,

particularly cattle, wade into the waterbody, linger to drink, and often urinate and defecate in the

water. This practice is now restricted for CAFOs; however, enforcement actions are the primary

means for reducing direct access, as described below (McFall, 2000).

In traditional farm production regions of the Midwest and Northeast, dairy barns and feedlots are

often in close proximity to streams or other water sources. This close proximity to streams was

formerly necessary in order to provide drinking water for the dairy cattle, to cool the animals in

hot weather via direct access, and to cool the milk prior to the widespread use of refrigeration. 

For CAFO-size facilities, this practice is now replaced with more efficient means of providing

drinking water for the dairy herd. In addition, the use of freestall barns and modern milking

centers minimizes the exposure of dairy cattle to the environment. For example, in New York

direct access of animals to surface water is more of a problem for the smaller, traditional dairy

farms that use older methods of housing animals. However, at these smaller facilities, direct

access to surface water has relatively lower impact on surface water compared with impacts

associated with silage leachate and milkhouse waste (Dimura, 2000).

In the arid West, feedlots are typically located near waterbodies to allow for cheap and easy stock 

watering. Many existing lots were configured to allow the animals direct access to the water. 

The direct deposition of manure and urine contributes greatly to water quality problems. 

Environmental problems associated with allowing farm animals access to waters that are adjacent

to the production area are well documented in the literature. EPA Region X staff have

documented dramatically elevated levels of Escherichia coli in rivers downstream of AFOs with

direct access to surface water. Recent enforcement actions against direct access facilities have

resulted in the assessment of tens of thousands of dollars in civil penalties (McFall, 2000).

2.3.2 Other Discharges to Surface Waters

Leaching to Ground Water 

Leaching of land-applied pollutants is a significant transport mechanism for water soluble

pollutants. In addition, leaking lagoons are a source of manure pollutants in ground water. 
2-19

Although manure solids purportedly “self-seal” lagoons to prevent ground water contamination,

some studies have shown otherwise. A study for the Iowa legislature published in 1999 indicates

that leaking is part of lagoon design standards and that all lagoons should be expected to leak

(Iowa State University, 1999). A survey of swine and poultry lagoons in the Carolinas found that

nearly two-thirds of the 36 lagoons sampled had leaked into the ground water (Meadows, 1995). 

Even clay-lined lagoons have the potential to leak, since they can crack or break as they age, and

can be susceptible to burrowing worms. In a three-year study of clay-lined swine lagoons on the

Delmarva Peninsula, researchers found that leachate from lagoons located in well-drained loamy

sand had a severe impact on ground water quality (Ritter and Chirnside, 1990).

Pollutant transport to ground water is also greater in areas with high soil permeability and

shallow water tables. Percolating water can transport pollutants to ground water, as well as to

surface waters via interflow. Contaminated ground water can deliver pollutants to surface waters

through hydrologic connections. Nationally, about 40 percent of the average annual stream flow

is from ground water (USEPA, 1993b). In the Chesapeake Bay watershed, the USGS estimates

that about half of the nitrogen loads from all sources to nontidal streams and rivers originate from

ground water (ASCE, 1998).

Understanding the connection between ground water and surface water is important when

developing surface water protection strategies, because ground water moves much more slowly

than surface water. For example, ground water in the Chesapeake Bay region takes an average of

10 to 20 years to reach the Bay; thus, it may take several decades to realize the full effect of

pollutant additions or reductions (ASCE, 1998).

Discharge to the Air and Subsequent Deposition

Atmospheric deposition can be a significant mechanism of transport to surface waters, as

nitrogen emissions to air can return to terrestrial or aquatic environments in dry form or dissolved

in precipitation (Agricultural Animal Waste Task Force, 1996). Discharges to air can occur as a

result of volatilization of pollutants already present in the manure, and of pollutants generated as

the manure decomposes. Ammonia is very volatile and can have significant impacts on water

quality through atmospheric deposition (Aneja et al., 1998). Ammonia losses from animal

feeding operations can be considerable, arising from manure piles, storage lagoons, and land

application fields. Other ways that manure pollutants can enter the air are from spray application

methods for land applying manure and from particulates wind-borne in dust.

The degree of volatilization of manure pollutants is dependent on the manure management

system. For example, losses are greater when manure remains on the land surface rather than

being incorporated into the soil and are particularly high when farmers perform spray application. 

Environmental conditions such as soil acidity and moisture content also affect the extent of

volatilization. Losses are reduced by the presence of growing plants (Follett, 1995).

Once airborne, pollutants can find their way into nearby streams, rivers, and lakes. The 1998

National Water Quality Inventory indicates that atmospheric deposition is the third largest cause

of water quality impairment for estuaries and the fifth largest cause of water quality impairment

for lakes, ponds, and reservoirs (USEPA, 2000a).
2-20

2.3.3 Pollutant-specific Transport

Nitrogen Compounds

Livestock waste can contribute up to 37 percent of total nitrogen loads to surface water (Mulla,

1999). Nitrogen compounds and nitrates in manure can reach surface water through several

pathways. As suggested by Follett (1995), agricultural nitrate contributions to surface water are

primarily from ground water connections and other subsurface flows. Although potentially less

significant, overland runoff can also carry nitrate to surface waters. A recent Iowa investigation

of chemical and microbial contamination near large-scale swine operations demonstrated the

presence of nitrate and nitrite not only in manure lagoons used to store swine waste before it is

land applied, but also in drainage ditches, agricultural drainage wells, tile line inlets and outlets,

and an adjacent river (CDCP, 1998).

Studies of small geographical areas have revealed evidence of nitrate contamination in ground

water. As of 1988, 40 percent of wells in the Chino Basin, California, had nitrate levels in excess

of the MCL; USEPA (1993b) identified dairy operations as the major source of contamination. 

This presents potentially widespread impacts, since water from the Chino Basin is used to

recharge the primary source of drinking water for residents of heavily populated Orange County. 

On the Delmarva peninsula, in Maryland, where poultry production is dominant, over 15 percent

of wells were found to have nitrate levels exceeding the MCL. Wells located close to chicken

houses contained the highest median nitrate concentrations (Ritter et al., 1989). Measured nitrate

levels in ground water beneath Delaware poultry houses are as high as 100 mg/L (Ritter et al.,

1989).

Elevated nitrate levels can also exist in surface waters, although these impacts are typically less

severe than ground water impacts. In a historical assessment, USGS (1997) found that nitrate

levels in streams in agricultural areas were elevated compared to undeveloped areas. 

Nevertheless, the in-stream nitrate concentrations were generally less than those for ground water

in similar locations, and the drinking water MCL was rarely exceeded. The primary exception to

this pattern was in the Midwest, where poorly drained soils restrict water percolation and

artificial drainage provides a quick path for nutrient-rich runoff to reach streams (USGS, 1997).

When farmers apply manure to land as fertilizer, risk of nitrate pollution generally increases at

higher rates of nitrogen application. Even when farmers land apply manure at agronomic rates,

nitrogen transport to surface water and ground water can still occur for the following reasons: (1)

nitrate is extremely mobile and may move below the plant root zone before being taken up; (2)

ammonia may volatilize and be redeposited in surface water; (3) the waste may be unevenly

distributed, resulting in local “hot spots”; (4) it may be difficult to obtain a representative sample

of the waste to determine the amount of mineralized (plant-available) nitrogen; (5) there are

uncertainties about the estimated rate of nitrogen mineralization in the applied waste; (6)

transport is affected by the manure application method (e.g., drip irrigation, spray irrigation,

knifing, etc.); and (7) transport is affected by uncontrollable environmental factors such as

rainfall and other local conditions (Follett, 1995).
2-21

Phosphorus Compounds

Phosphorus can reach surface waters via discharges directly into surface water and runoff of

manure to surface water from feedlots, and via runoff and erosion from land application sites. 

The organic phosphorus compounds in manure are generally water soluble and subject to

leaching and dissolution in runoff (Gerritse, 1977). Once in receiving waters, these compounds

can undergo transformation and become available to aquatic plants. Overall, land-applied

phosphorus is less mobile than nitrogen, since the mineralized (inorganic phosphate) form is

easily adsorbed to soil particles. A report by the Agricultural Research Service noted that

phosphorus bound to eroded sediment particles makes up 60 to 90 percent of phosphorus

transported in surface runoff from cultivated land (USDA/ARS, 1999). For this reason, most

agricultural phosphorus control measures have focused on soil erosion control to limit transport

of particulate phosphorus. However, soils do not have infinite phosphate adsorption capacity,

and dissolved inorganic phosphates can still enter waterways via runoff even if soil erosion is

controlled (National Research Council, 1993). 

Livestock waste can contribute up to 65 percent of total phosphorus loads in surface waters

(Mulla, 1999). Animal wastes typically have lower N:P ratios than crop N:P requirements, such

that application of manure at a nitrogen-based agronomic rate can result in application of

phosphorus at several times the agronomic rate (Sims, 1995). Summaries of soil test data in the

United States confirm that many soils in areas dominated by animal-based agriculture have

excessive levels of phosphorus (Sims, 1995). Research also indicates that there is a potential for

phosphorus to leach into ground water through sandy soils with already high phosphorus content

(Citizens Pfiesteria Action Commission, 1997).

Ammonia

Ammonia can reach surface waters in a number of ways, including discharge directly to surface

waters, leaching, dissolution in surface runoff, erosion, and atmospheric deposition. Leaching

and runoff are generally not significant transport mechanisms for ammonia compounds in landapplied manure, because ammonium can be sorbed to soils (particularly those with high cation

exchange capacity), incorporated (fixed) into clay or other soil complexes, or transformed into

organic form by soil microbes (Follett, 1995). However, in these forms, erosion can transport

nitrogen to surface waters. A recent Iowa investigation of chemical and microbial contamination

near large-scale swine operations demonstrated the presence of ammonia not only in manure

lagoons used to store swine waste before it is land applied, but also in drainage ditches,

agricultural drainage wells, tile line inlets and outlets, and an adjacent river (CDCP, 1998).

Ammonia losses from animal feeding operations to the air and subsequent deposition to surface

waters can be considerable, arising from sources such as manure piles, storage lagoons, and land

application fields. For example, in North Carolina, animal agriculture is responsible for over 90

percent of all ammonia emissions (Aneja et al., 1998). Ammonia composes more than

40 percent of the total estimated nitrogen emissions from all sources (Aneja et al., 1998). 

Furthermore, data from Sampson County, North Carolina, indicate that ammonia levels in rain

have increased with increases in the size of the pork industry. Levels more than doubled between

1985 and 1995 (Aneja et al., 1998). Based on EPA estimates, swine operations in eastern North
2-22

Carolina were responsible for emissions of 135 million pounds of nitrogen per year as of 1995. 

If deposited in a single basin, this would result in nitrogen loadings of almost 2.1 million pounds

of nitrogen per year (Nowlin et al., 1997).

Pathogens

Sources of pathogen contamination from AFOs include surface discharges and lagoon leachate. 

Surface runoff from land application fields can be a source of pathogen contamination,

particularly if a rainfall event occurs soon after application or if the land is frozen or snowcovered (Mulla, 1999). Researchers have reported concentrations of bacteria in runoff water

from fields treated with poultry litter at several orders of magnitude above contact standards

(Giddens and Barnett, 1980; Coyne and Blevins, 1995).

A recent Iowa investigation of chemical and microbial contamination near large-scale swine

operations demonstrated the presence of pathogens not only in manure lagoons used to store

swine waste before it is land applied, but also in drainage ditches, agricultural drainage wells, tile

line inlets and outlets, and an adjacent river (CDCP, 1998). Also, studies have reported that

lands receiving fresh manure application can be the source of up to 80 percent of the fecal

bacteria in surface waters (Mulla, 1999). Similarly, both Cryptosporidium parvum and Giardia

species have also been found in over 80 percent of 66 surface water sites tested (LeChevallier et

al., 1991). Since these protozoa do not multiply outside of the host, livestock animals are one

potential source of this contamination. The bacterium Erysipelothrix spp., primarily a swine

pathogen, has been isolated from many fish and avian species (USFWS, 2000).

High levels of indicator bacteria in surface water near CAFOs have been documented. For

instance, Zirbser (1998) documented a report of fecal coliform counts of 3,000/100 ml and fecal

streptococci counts over 30,000/100 ml downstream from a swine waste lagoon site. (No

sampling was performed upstream of the lagoon site.) Fecal coliform pollution from treated and

partially treated sewage and storm water runoff is often cited in beach closures and shellfish

restrictions.

The natural filtering and adsorption action of soils typically causes a majority of the

microorganisms in land-applied manure to be stranded at the soil surface (Crane et al., 1980). 

This phenomenon helps protect underlying ground water but increases the likelihood of runoff

losses to surface waters. Pathogens discharged to the water column can subsequently adsorb to

sediments, presenting a long-term health hazard. Benthic sediments harbor significantly higher

concentrations of bacteria than the overlying water column (Mulla, 1999). When the bottom

stream is disturbed, as when animals have direct access to a stream, the sediment releases

bacteria back into the water column (Sherer et al., 1988, 1992). 

While surface waters are typically more prone to pathogen contamination than ground waters,

subsurface flows may also be a mechanism for pathogen transport depending on weather, site,

and operating conditions. Ground waters in areas of sandy soils, limestone formations, or

sinkholes are particularly vulnerable. For example, the bacteria Clostridium perfringens was

detected in the ground water below plots of land treated with swine manure, and fecal coliform

has been detected in ground water beneath soil amended with poultry manure (Mulla, 1999). In
6

GAO reviewed compliance data from 1993 through 1996, from more than 17,000 community water

systems, in California, Illinois, Nebraska, New Hampshire, North Carolina, and Wisconsin.

7

The 15 percent figure is from a 1996 study of Nebraska wells by the Nebraska Department of Health and

University of Nebraska; the 42 percent figure is from the EPA National Statistical Assessment of Rural Water

Conditions (1984).

2-23

1998, Campylobacter jejuni was isolated from ground water, and some of the strains were the

same type as those from a dairy farm in the same hydrologic area (Stanley et al., 1998).

There are other accounts of high levels of micoorganisms in ground water near feedlots. In cow

pasture areas of Door County, Wisconsin, where a thin topsoil layer is underlain by fractured

limestone bedrock, ground water wells have commonly been shut down due to high bacteria

levels (Behm, 1989). For example, a well at one rural household produced brown, manure-laden

water (Behm, 1989). Private wells are more prone to contamination than public wells, since they

tend to be shallower and therefore more susceptible to contaminants leaching from the surface. 

In a survey of drinking water standard violations in six states over a four-year period, the U.S.

General Accounting Office (USGAO, 1997) found that bacterial standard violations occurred in

3 to 6 percent of community water systems each year.6

 By contrast, USGAO reported that some

bacterial contamination occurred in 15 to 42 percent of private wells, according to statistically

representative assessments performed by others.7

Several factors affect the likelihood of disease transmission by pathogens in animal manure,

including pathogen survivability in the environment. For example, Salmonella can survive in the

environment for nine months or more, providing for increased dissemination potential (USFWS,

2000); and Campylobacter can remain dormant, making water an important vehicle for

campylobacteriosis (Altekruse, 1998). Recent studies are better characterizing the survivability

and transport of pathogens in manure once it has been land applied. Several researchers (Dazzo

et al., Himathongkham et al., 1999; Kudva et al., 1998; Maule, 1999; Van Donsel et al., 1967)

found that soil type, manure application rate, temperature, moisture level, aeration, soil pH, and

the amount of time that manure is held before it is applied to pastureland are dominating factors

in bacteria survival.

Experiments on land-applied poultry manure (Crane et al., 1980) indicated that the population of

fecal organisms decreases rapidly as manure is heated, dried, and exposed to sunlight on the soil

surface. However, regrowth of fecal organisms also occurred in these experiments. More recent

research indicated that pathogens can survive in manure for 30 days or more (Himathongkham et

al., 1999; Kudva et al., 1998; Maule, 1999). Kudva found that Escherichia coli survived for 47

days in aerated cattle manure piles that were exposed to outdoor weather; drying the manure

reduced the number of viable pathogens. Stehman (2000) also notes that Escherichia coli

O157:H7, Cryptosporidium parvum, and Giardia can survive and remain infectious in surface

waters for a month or more.

The continued application of waste on a particular area could lead to extended pathogen survival

and buildup (Dazzo et al., 1973). Additionally, repeated applications and/or high application

rates increase the likelihood of runoff to surface water and transport to ground water.
8

In a series of experiments, Edwards and Daniel (1992b, 1993a,b, as reported by Daniel et al., 1995)

measured runoff from fescue grass plots treated with poultry litter, poultry manure slurry, and swine manure slurry

to determine how runoff quality is impacted by application rate and rain intensity. They found that for all wastes,

the application rate had a significant effect on the runoff concentration and mass loss of COD (as well as other

constituents). 

9

EPA assumes that 175 lb N/acre is a typical requirement for a fescue crop in Arkansas, based on

information from U.S. Department of Agriculture extension agents (Tetra Tech, 2000b).

2-24

Organic Matter

Discharge and runoff of manure from feedlots cause large loadings of organic matter to surface

waters. There have been numerous incidents of discharges from AFOs nationwide directly to

surface waters (see Chapter 4). Discharges can also originate from land application sites when

farmers over-apply or misapply manure. Even if farmers apply manure such that there is not a

concentrated discharge, organic matter will be present in runoff from land application sites. As

shown by Daniel et al. (1995), runoff of organic matter increases as application rate increases.8

For example, Daniel et al. (1995) reported that when the swine manure slurry application rate

increased from 193 lb N/acre to 387 lb N/acre,9 COD levels in runoff (generated from a rainfall

intensity of 2 inches/hour) increased from 282 mg/L to 504 mg/L. By comparison, runoff from a

control plot yielded 78 mg/L COD.

Salts and Trace Elements

Salts can reach surface waters via discharges from feedlots and runoff from land application

sites. Salts can also leach into ground water and subsequently reach surface water. Trace

elements can also be transported by these mechanisms. A recent Iowa investigation showed that

trace elements were present not only in manure lagoons used to store swine waste before land

application, but also in drainage ditches, agricultural drainage wells, tile line inlets and outlets,

and an adjacent river (CDCP, 1998). Selenium concentrations have been detected in swine

manure lagoons at up to 6 μg/L, copper has been detected in liquid swine manure prior to land

application at 15 mg/L, and zinc has been detected in soils that receive applications of cattle

manure at levels up to 9.5 mg/kg in the upper 60 centimeters of soil (USFWS, 2000).

Antibiotics

Little information is available regarding the fate and transport properties of antibiotics, or the

potential releases from animal waste compared to other sources such as municipal and industrial

wastewaters, septic tank leachate, runoff from land-applied sewage sludge, crop runoff, and

urban runoff. However, it is known that the primary mechanisms of eliminating antibiotics from

livestock are through urine and bile. Also, essentially all of an antibiotic administered to an

animal is eventually excreted, whether unchanged or in metabolite form (Tetra Tech, 2000a).

Although the presence of excreted antibiotics themselves may be of concern, the development of

antibiotic-resistant pathogens due to exposure to environmental levels of antibiotics is generally

of greater concern. The risk for development of antibiotic-resistant pathogens from this exposure

is unknown.
2-25

Hormones

Hormones can reach surface waters through the same routes as other manure pollutants,

including runoff and erosion as well as direct contact of animals with the water. Considering

specific hormones used, however, estrogen is more likely to be lost by runoff than leaching,

while testosterone is lost mainly through leaching (Shore et al., 1995).

Several sites have documented the presence of hormones in runoff and surface waters. For

example, runoff from a field receiving poultry litter was found to contain estrogen. Also, an

irrigation pond and three streams in the Conestoga River watershed near the Chesapeake Bay had

both estrogen and testosterone. Each of these sites were affected by fields receiving poultry litter

(Shore et al., 1995). Runoff from fields with land-applied manure has been reported to contain

estrogens, estradiol, progesterone, and testosterone, as well as their synthetic counterparts. 

Estrogens have also been found in runoff from heavily grazed land (Addis et al., 1999).

Other Pollutants

There has been almost no research on losses of pesticides in runoff from manured lands. A 1999

literature review by the University of Minnesota discussed a 1994 study showing that losses of

cyromazine (used to control flies in poultry litter) in runoff increased with the rate of poultry

manure application and the intensity of rainfall. The 1999 literature review also includes a 1995

study documenting that about 1 percent of all pesticides enter surface water. However, the

magnitude of the impacts of these losses on surface water are unknown (Mulla, 1999). In

general, little information is available regarding the fate and transport of pesticides or their

bioavailability in waste-amended soils. Furthermore, there is little information comparing

potential releases of these compounds from animal waste to other sources such as municipal and

industrial wastewaters, septic tank leachate, runoff from land-applied sewage sludge, crop runoff,

and urban runoff.
2-26
3-1

3. POTENTIAL HAZARDS FROM AFO POLLUTANTS

As described in Chapter 2, animal feeding operations are associated with a variety of pollutants,

including nutrients (specifically nitrogen and phosphorus), ammonia, pathogens, organic matter,

salts, trace elements, solids, antibiotics, hormones, gas and particulate emissions, and pesticides. 

These AFO pollutants can produce multimedia impacts, such as the following:

C Surface water. Impacts have been associated with surface discharges of waste, as

well as leaching to ground water and subsurface flow to surface water. Generally,

states with high concentrations of feedlots experience 20 to 30 serious water quality

pollution problems per year involving manure lagoon spills and feedlot runoff (Mulla,

1999). The waste’s oxygen demand and ammonia content can result in fish kills and

reduced biodiversity. Solids can increase turbidity and impact benthic organisms. 

Nutrients contribute to eutrophication and associated algae blooms. Algal decay and

nighttime respiration can depress dissolved oxygen levels, potentially leading to fish

kills and reduced biodiversity. Eutrophication is also a factor in blooms of toxic algae

and other toxic microorganisms, such as Pfiesteria piscicida. Human and animal

health impacts are primarily associated with drinking contaminated water (pathogens

and nitrates), coming into contact with contaminated water (pathogens such as toxic

algae and Pfiesteria), and consuming contaminated shellfish (pathogens such as toxic

algae). Trace elements (e.g., arsenic, copper, selenium, and zinc) may also present

human health and ecological risks. Salts contribute to salinization and disruption of

ecosystem balance, as well as degradation of drinking water supplies. Antibiotics,

pesticides, and hormones may have low-level, long-term ecosystem effects.

C Ground water. Impacts have been associated with pollutants leaching to ground

water. Human and animal health impacts are associated with pathogens and nitrates

in drinking water. Leaching salts can increase health risks to salt-sensitive

individuals, and can make the water unpalatable. Trace elements, antibiotics,

pesticides, and hormones may also present human health and ecological risks through

ground water pathways.

C Air. Air impacts include human health effects from ammonia, hydrogen sulfide, other

odor-causing compounds, particulates, and the contribution to global climate change

due to methane emissions. In addition, volatilized ammonia can be redeposited on the

earth and contribute to eutrophication. 

C Soil. Trace elements and salts in animal manure can accumulate in soil and become

toxic to plants. Salts also deteriorate soil quality by leading to reduced permeability

and overall poor physical condition. Crops may provide a human and animal

exposure pathway for trace elements and pathogens.

This chapter describes in greater detail the known or potential adverse human health and

ecological effects of AFO pollutants.
3-2

3.1 PRIMARY NUTRIENTS

This section reviews the hazards posed by primary nutrients in animal manure. It focuses on

nitrogen and phosphorus, which have received the greatest attention in the scientific literature. 

Actual or anticipated levels of potassium in ground water and surface water are unlikely to pose

hazards to aquatic life or human health (Wetzel, 1983). Potassium does contribute to salinity,

however, and applications of high salinity manure are likely to decrease the fertility of the soil.

3.1.1 Ecology

Eutrophication

Eutrophication is the process in which phosphorus and nitrogen over-enrich a waterbody and

disrupt the balance of life in that waterbody. Perhaps the most documented impact of nutrient

pollution is the increase in surface water eutrophication (nutrient enrichment) and its effects on

aquatic ecosystems (Vallentyne, 1974). Although nutrients are essential for the growth of

phytoplankton (free-floating algae), periphyton (attached algae), and aquatic plants, which form

the base of the aquatic food web, the overabundance of nutrients can lead to harmful algal

blooms and other adverse effects, such as:

C Increased biomass of phytoplankton;

C Shifts in phytoplankton to bloom-forming species that may be toxic or inedible;

C Changes in macrophyte species composition and biomass;

C Death of coral reefs and loss of coral reef communities;

C Decreases in water transparency;

C Taste, odor, and water treatment problems;

C Oxygen depletion;

C Increased incidence of fish kills;

C Loss of desirable fish species;

C Reductions in harvestable fish and shellfish; and

C Decreases in aesthetic value of the waterbody (Carpenter et al., 1998).

The type of waterbody impacted may dictate which nutrient (nitrogen or phosphorus) will have

the most impact. In estuaries and coastal marine waters, nitrogen is typically the limiting nutrient

(i.e., in these waters, phosphorus levels are sufficiently high compared to nitrogen such that small

changes in nitrogen concentrations have a greater effect on plant growth). In fresh waters,

phosphorus is typically the limiting nutrient (Wendt and Corey, 1980; Robinson and Sharpley,

1995). There can be exceptions to this generalization, however, especially in waterbodies with

heavy pollutant loads. For example, estuarine systems may become phosphorus-limited when

nitrogen concentrations are high. In such cases, excess phosphorus will produce algal blooms

(North Carolina’s Nicholas School of the Environment's Agricultural Animal Waste Task Force,

1994). Thus, both nitrogen and phosphorus loads can contribute to eutrophication in either water

type.
3-3

Algae and Other Toxic Microorganisms

Eutrophication causes the enhanced growth and subsequent decay of algae, which can lower

dissolved oxygen content of a waterbody to levels insufficient to support fish and invertebrates. 

In some cases, this situation can produce large areas devoid of life because of a lack of sufficient

dissolved oxygen. One extreme example is the “Dead Zone,” an area of hypoxic water larger

than 10,000 km2

 that spreads off the Louisiana coast in the Gulf of Mexico each summer. The

Dead Zone is believed to be caused by excess chemical fertilizer; however, nutrients from animal

waste have also contributed to the problem. This condition has been attributed to excess

nutrients delivered primarily by the Mississippi and Atchafalaya river systems (Atwood et al.,

1994). The problem in the Gulf demonstrates that pollutant discharges can have far-reaching

downstream impacts. In fact, the nutrient loadings to the Gulf originate from sources over a large

land area covering approximately 41 percent of the conterminous United States (Goolsby et al.,

1999).

Eutrophication can also affect phytoplankton and zooplankton population diversity, abundance,

and biomass, and increase the mortality rates of aquatic species. For example, floating algal mats

can prevent sunlight from reaching submerged aquatic vegetation, which serves as habitat for fish

spawning, juvenile fish, and fish prey (e.g., aquatic insects). The resulting decrease in

submerged aquatic vegetation adversely affects both fish and shellfish populations (USEPA,

2000a).

Another effect of eutrophication is increased incidence of harmful algal blooms, which release

toxins as they die and can severely impact wildlife as well as humans. In marine ecosystems,

blooms known as red or brown tides have caused significant mortality in marine mammals

(Carpenter et al., 1998). In fresh water, cyanobacterial toxins have caused many incidents of

poisoning of wild and domestic animals that have consumed impacted waters (Health Canada

Environmental Health Program, 1998). Published reports of wildlife poisoning from these

blooms include amphibians, fish, snakes, waterfowl, raptors, and deer (USFWS, 2000).

Eutrophication is also associated with blooms of other toxic organisms, such as the estuarine

dinoflagellate Pfiesteria piscicida. Pfiesteria has been implicated as the primary causative agent

of many major fish kills and fish disease events in North Carolina estuaries and coastal areas

(NCSU, 2000), as well as in Maryland and Virginia tributaries to the Chesapeake Bay (USEPA,

1997b). Pfiesteria often lives as a nontoxic predatory animal, becoming toxic in response to

human influences including excessive nutrient enrichment (NCSU, 2000). While nutrientenriched conditions are not required for toxic outbreaks to occur, excessive nutrient loadings are

a concern because they help create an environment rich in microbial prey and organic matter that

Pfiesteria uses as a food supply. By increasing the concentration of Pfiesteria, nutrient loads

increase the likelihood of a toxic outbreak when adequate numbers of fish are present (Citizens

Pfiesteria Action Commission, 1997). Researchers have documented stimulation of Pfiesteria

growth by human sewage and swine effluent spills and have shown that the organism’s growth

can be highly stimulated by both inorganic and organic nitrogen and phosphorus enrichments

(NCSU, 2000).
10 Brown blood disease is named for the color of the blood of dead or dying fish, indicating that the

hemoglobin has been converted to methemoglobin.

3-4

Increased algal growth can also raise the pH of waterbodies, as algae consume dissolved carbon

dioxide to support photosynthesis. Many biological processes, including reproduction, cannot

function in water that is very acidic or alkaline (USEPA, 2000a).

Nitrites

Nitrites can also pose a risk to aquatic life: if sediments are enriched with nutrients, the

concentrations of nitrites in the overlying water may be raised enough to cause nitrite poisoning

or “brown blood disease”10 in fish (USDA, 1992). In addition, excess nitrogen can contribute to

water quality decline by increasing the acidity of surface waters.

3.1.2 Human Health

Nitrates/Nitrites

The main hazard to human health from primary nutrients is elevated nitrate levels in drinking

water. In particular, infants are at risk from nitrate poisoning (also referred to as

methemoglobinemia or “blue baby syndrome”), which can be fatal. This poisoning results in

oxygen starvation and is due to nitrite (a metabolite of nitrate), which is formed in the

environment, foods, and the human digestive system. Compared to adults and older children,

infants under six months experience elevated nitrite production because their digestive systems

have a higher concentration of nitrate-reducing bacteria. Nitrite oxidizes iron in the hemoglobin

of red blood cells to form methemoglobin, which cannot carry sufficient oxygen to the body’s

cells and tissues. Although methemoglobin is continually produced in humans, an enzyme in the

human body reduces methemoglobin back to hemoglobin. In most individuals, this conversion

occurs rapidly. Infants, however, have a low concentration of methemoglobin-reducing enzyme,

as do individuals with an enzyme deficiency. In these people, methemoglobin is not converted to

hemoglobin as readily (Nebraska Cooperative Extension, 1995).

Because infants under six months have a higher concentration of digestive bacteria that reduce

nitrates, and a lower concentration of methemoglobin-reducing enzyme, they are at higher risk

for methemoglobinemia (Nebraska Cooperative Extension, 1995). To protect infant health, the

EPA set drinking water Maximum Contaminant Levels (MCLs) of 10 mg/L for nitrate-nitrogen

and 1 mg/L for nitrite-nitrogen. MCLs are the maximum permissible levels of pollutants allowed

in water delivered to public drinking water systems. Once a water source is contaminated, the

costs of protecting consumers from nitrate exposure can be significant. Nitrate is not removed by

conventional drinking water treatment processes. Its removal requires additional, relatively

expensive treatment units.

Although reported cases of methemoglobinemia are rare, the incidence of actual cases may be

greater than the number reported. Studies in South Dakota and Nebraska have indicated that

most cases of methemoglobinemia are not reported (Michel et al., 1996; Meyer, 1994). For

example, in South Dakota between 1950 and 1980, only two cases were reported, while at least
3-5

80 were estimated to have occurred (Meyer, 1994). There are at least two reasons for this

underreporting. First, methemoglobinemia can be difficult to detect in infants because its

symptoms are similar to other conditions (Michel et al., 1996). In addition, doctors are not

always required to report it (Michel et al., 1996). 

In addition to blue baby syndrome, low blood oxygen due to methemoglobinemia has also been

linked to birth defects, miscarriages, and general poor health in humans and animals. These

effects are exacerbated by concurrent exposure to many species of bacteria in water (IRIS, 2000). 

Studies in Australia found an increased risk of congenital malformations with consumption of

high-nitrate ground water (Bruning-Fann and Kaneene, 1993). Multi-generation animal studies

have found decreases in birth weight, post-natal growth, and organ weights among mammals

prenatally exposed to nitrite (IRIS, 2000). Nitrate- and nitrite-containing compounds may also

cause hypotension or circulatory collapse (Bruning-Fann and Kaneene, 1993).

High nitrate levels in drinking water have also been implicated in higher rates of stomach and

esophageal cancer, although a 1995 National Research Council report concludes that exposure to

nitrate and nitrite concentrations in drinking water are unlikely to contribute to human cancer

risks (National Research Council, 1995). However, nitrate metabolites such as N-nitroso

compounds (especially nitrosamines) have been linked to severe human health effects such as

gastric cancer (Bruning-Fann and Kaneene, 1993). The formation of N-nitroso compounds

occurs in the presence of catalytic bacteria (e.g., those found in the stomach) or thiocyanate.

Generally, people drawing water from domestic wells are at greater risk of nitrate poisoning than

those drawing from public wells (Nolan and Ruddy, 1996), since domestic wells are typically

shallower and not subject to wellhead protection or monitoring requirements. Reported cases of

methemoglobinemia are most often associated with wells that were privately dug and that may

have been badly positioned in relation to the disposal of human and animal excreta (Addiscott et

al., 1991). Furthermore, people served by public systems are better protected even if the water

becomes contaminated, due to water quality monitoring and treatment requirements.

Phosphorus

Animal manure also contributes to increased phosphorus concentrations in water supplies. 

Previous evaluations of phosphorus have not identified significant adverse human health effects,

but phosphate levels greater than 1.0 mg/L may interfere with coagulation in drinking water

treatment plants and thereby increase treatment costs (North Carolina’s Nicholas School of the

Environment's Agricultural Animal Waste Task Force, 1994).

Eutrophication/Algal Blooms

To the extent that nitrogen and phosphorus contribute to algal blooms in surface water through

accelerated eutrophication as described in Section 3.1.1, these nutrients can reduce the aesthetic

and recreational value of surface water resources. Algae can affect drinking water by clogging

treatment plant intakes, producing objectionable tastes and odors. Algae can also increase

production of harmful chlorinated byproducts (e.g., trihalomethanes) by reacting with chlorine
3-6

used to disinfect drinking water. These impacts result in increased costs of drinking water

treatment, reduced drinking water quality, and/or increased health risks.

Eutrophication can also affect human health by enhancing growth of harmful algal blooms that

release toxins as they die. In marine ecosystems, harmful algal blooms such as red tides can

result in human health impacts via shellfish poisoning and recreational contact (Thomann and

Mueller, 1987). In fresh water, blooms of cyanobacteria (blue-green algae) may pose a serious

health hazard to humans via water consumption. When cyanobacterial blooms die or are

ingested, they release water-soluble compounds that are toxic to the nervous system and liver

(Carpenter et al., 1998).

In addition, eutrophication is associated with blooms of a variety of other organisms that are

toxic to humans, such as the estuarine dinoflagellate Pfiesteria piscicida. While Pfiesteria is

primarily associated with fish kills and fish disease events, the organism has also been linked

with human health impacts through dermal or inhalation exposure. Researchers working with

dilute toxic cultures of Pfiesteria exhibited symptoms such as skin sores, severe headaches,

blurred vision, nausea/vomiting, sustained difficulty breathing, kidney and liver dysfunction,

acute short-term memory loss, and severe cognitive impairment (NCSU, 2000). People with

heavy environmental exposure have exhibited symptoms as well. In a 1998 study, such

environmental exposure was definitively linked with cognitive impairment and less consistently

linked with physical symptoms (Morris et al., 1998).

3.2 AMMONIA

3.2.1 Ecology

Ammonia exerts a direct biochemical oxygen demand (BOD) on the receiving water. As

ammonia is oxidized, dissolved oxygen is consumed. Moderate depressions of dissolved oxygen

are associated with reduced species diversity, while more severe depressions can produce fish

kills. In fact, ammonia is a leading cause of fish kills (USDA, 1992). Ammonia-induced fish

kills are a potential consequence of the discharge of animal wastes directly to surface waters. For

example, in a May 1997 incident in Wabasha County, Minnesota, ammonia in a dairy cattle

manure discharge killed 16,500 minnows and white suckers (Clean Water Action Alliance,

1998). Additionally, ammonia loadings can contribute to accelerated eutrophication of surface

waters, which can significantly impact aquatic ecosystems in a number of ways, as noted above.

3.2.2 Human Health

Ammonia is a nutrient form of nitrogen that can have several impacts. First, volatilized

ammonia is of concern because of direct localized impacts on air quality. Ammonia produces an

objectionable odor and can cause nasal and respiratory irritation.

In addition, ammonia contributes to eutrophication of surface waters. This phenomenon is

primarily a hazard to aquatic life but is also associated with human health impacts (see Section

3.1.2). As previously mentioned, eutrophication reduces the aesthetic and recreational value of

water bodies. Additionally, the associated algae blooms can affect drinking water by clogging
3-7

treatment plant intakes, producing objectionable tastes and odors, and increasing production of

harmful chlorinated byproducts. These impacts result in increased drinking water treatment

costs, reduced drinking water quality, and/or increased health risks. Eutrophication can also

impact human health by enhancing the growth of toxic algae and other toxic organisms. 

3.3 PATHOGENS

3.3.1 Ecology

Animal wastes carry parasites, bacteria, and viruses, many of which have the potential to be

harmful to wildlife (USDA, 1992; Jackson et al., 1987). Some bacteria in livestock waste cause

avian botulism and avian cholera, which have killed thousands of migratory waterfowl in the past

(USEPA, 1993b). Avian botulism is a food poisoning caused by ingestion of a neurotoxin

produced by the bacterium Clostridium botulinum type C., and Salmonella spp, both of which

naturally occur in the intestinal tract of warm-blooded animals (USFWS, 2000).

Pathogens in surface water can adhere to the skin of fish or be taken up internally when present at

high enough concentrations. In a controlled experiment, Fattal et al. (1992) detected significant

bacterial concentrations in fish exposed to Escherichia coli and other microorganisms for up to

48 hours. The data suggest that harmful pathogens could be taken up by fish-eating carnivores

feeding in contaminated surface waters.

Shellfish are filter feeders that pass large volumes of water over their gills. As a result, they can

concentrate a broad range of microorganisms in their tissues (Chai et al., 1994). This provides a

pathway for pathogen transmission to higher trophic organisms. However, little information is

available to assess the health effects of contaminated shellfish on wildlife receptors.

3.3.2 Human Health

Pathogens may be transmitted to humans through contaminated surface water or ground water

used for drinking, or by direct contact with contaminated surface water through recreational uses. 

By the year 2010, about 20 percent of the human population (especially infants, the elderly, and

those with compromised immune systems) will be classified as particularly vulnerable to the

health effects of pathogens (Mulla, 1999). Over 150 pathogens in livestock manure are

associated with risks to humans (CAST, 1992). Exhibit 3-1 presents a list of several of these

pathogens and their associated diseases, including salmonellosis, cryptosporidiosis, and

giardiasis. Other pathogens that have been associated with livestock waste include those that

cause cholera, typhoid fever, and polio (USEPA, 1993b). Many of these pathogens are

transmitted to humans via the fecal-oral route. In the water environment, humans may be

exposed to pathogens through consumption of contaminated drinking water (although the EPA

assumes adequate drinking water treatment of public supplies), or by incidental ingestion during

recreational activities in contaminated waters.
3-8

EXHIBIT 3-1

Some Diseases and Parasites Transmittable to Humans from Animal Manure a

Disease Responsible Organism Symptoms

Bacteria

Anthrax Bacillus anthracis Skin sores, fever, chills, lethargy, headache,

nausea, vomiting, shortness of breath, cough,

nose/throat congestion, pneumonia, joint stiffness,

joint pain

Brucellosis Brucella abortus, Brucella

melitensis, Brucella suis

Weakness, lethargy, fever, chills, sweating,

headache

Colibaciliosis Escherichia coli (some serotypes) Diarrhea, abdominal gas 

Coliform mastitismetritisEscherichia coli (some serotypes) Diarrhea, abdominal gas 

Erysipelas Erysipelothrix rhusiopathiae Skin inflammation, rash, facial swelling, fever,

chills, sweating, joint stiffness, muscle aches,

headache, nausea, vomiting

Leptospirosis Leptospira pomona Abdominal pain, muscle pain, vomiting, fever

Listeriosis Listeria monocytogenes Fever, fatigue, nausea, vomiting, diarrhea

Salmonellosis Salmonella species Abdominal pain, diarrhea, nausea, chills, fever,

headache

Tetanus Clostridium tetani Violent muscle spasms, “lockjaw” spasms of jaw

muscles, difficulty breathing

Tuberculosis Mycobacterium tuberculosis,

Mycobacterium avium

Cough, fatigue, fever, pain in chest, back, and/or

kidneys

Rickettsia

Q fever Coxiella burneti Fever, headache, muscle pains, joint pain, dry

cough, chest pain, abdominal pain, jaundice

Viruses

Foot and Mouth virus Rash, sore throat, fever

Swine Cholera virus

New Castle virus

Psittacosis virus Pneumonia

Fungi

Coccidioidomycosis Coccidioides immitus Cough, chest pain, fever, chills, sweating,

headache, muscle stiffness, joint stiffness, rash,

wheezing

Histoplasmosis Histoplasma capsulatum Fever, chills, muscle ache, muscle stiffness,

cough, rash, joint pain, joint stiffness 

Ringworm Various microsporum and

trichophyton

Itching, rash

Protozoa

Balantidiasis Balatidium coli
EXHIBIT 3-1

Some Diseases and Parasites Transmittable to Humans from Animal Manure a

Disease Responsible Organism Symptoms

3-9

Coccidiosis Eimeria species Diarrhea, abdominal gas

Cryptosporidiosis Cryptosporidium parvum Watery diarrhea, dehydration, weakness,

abdominal cramping

Giardiasis Giardia lamblia Diarrhea, abdominal pain, abdominal gas, nausea,

vomiting, headache, fever

Toxoplasmosis Toxoplasma species Headache, lethargy, seizures, reduced cognitive

function

Parasites/Metazoa

Ascariasis Ascaris lumbricoides Worms in stool or vomit, fever, cough, abdominal

pain, bloody sputum, wheezing, skin rash,

shortness of breath

Sarcocystiasis Sarcosystis species Fever, diarrhea, abdominal pain

Sources: Diseases and organisms were compiled from USDA/NRCS (1996) and USEPA (1998). Symptom

descriptions were obtained from various medical and public health service Internet sites.

a

 Pathogens in animal manure are a potential source of disease in humans and other animals. This list represents a

sampling of diseases that may be transmittable to humans.

Although a wide range of organisms may cause disease in humans, relatively few microbial

agents are responsible for the majority of human disease outbreaks from water-based exposure

routes. This point is illustrated by Exhibit 3-2, which presents reports of waterborne disease

outbreaks and their causes (if known) in the United States for the period 1989-1996. Intestinal

infections are the most common type of waterborne infection, and affect the most people. 

As presented in Exhibit 3-2, most reported outbreaks were associated with protozoa and bacteria. 

As noted in Exhibit 3-1, Cryptosporidium parvum can produce gastrointestinal illness, with

symptoms such as severe diarrhea. Relatively low doses of both Cryptosporidium parvum as

well as Giardia species are needed to cause infection (Stehman, 2000). Although healthy people

typically recover relatively quickly (within 2 to 10 days) from this type of illness, these diseases

can be fatal in people with weakened immune systems. These individuals typically include

children, the elderly, people with human immunovirus (HIV) infection, chemotherapy patients,

and those taking medications that suppress the immune system.
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EXHIBIT 3-2

Etiology of Waterborne Disease Outbreaks Causing Gastroenteritis 1989-1996

Type of

Organism Etiologic Agent

Total

Number of

Outbreaks

Outbreaks

Associated with

Drinking Water

Outbreaks 

Associated with

Recreational Water

Surface Ground Natural Pool/

Park

Protozoa

Giardia spp. 27 12 6 4 5

Cryptosporidium parvum 21 4 4 2 11

Bacteria with

Potential for

Infecting

Multiple

Species

Escherichia coli O157:H7 11 - 3 7 1

Campylobacter jejuni 3 3 -- -

Salmonella typhimurium 1 - 1- -

Salmonella java 1 - -- 1

Leptospira grippotyphosa 1 - -1 -

Bacterial

Infections

Associated

with Humans

Shigella sonnei 17 - 7 10 -

Shigella flexneri 2 - 11 -

Human

viruses

Hepatitis A 3 - - - 3

Norwalk virus 1 - 1 - -

Norwalk-like virus 1 - - - 1

Small round structured

virus

1 1 -- -

Acute

Gastroenteritis

Unidentified etiologymany consistent with viral

epidemiology

60 8 44 7 1

Other Cyanobacteria-like bodies 1 1 - - -

Source: Stehman, 2000.

Exhibit 3-2 shows that infections caused by Giardia species and Cryptosporidium parvum

(considered the two most important waterborne protozoa) were the leading causes of infectious

waterborne disease outbreaks in which an agent was identified, both for total cases and for

number of outbreaks (Mulla, 1999; Stehman, 2000). In 1993 in Milwaukee, Wisconsin,

Cryptosporidium parvum contamination of a public water supply caused more than 100 deaths

and an estimated 403,000 illnesses (Smith, 1994; Casman, 1996). The outbreak cost an

estimated $37 million in lost wages and productivity (Smith, 1994). The source of the oocysts

was not identified, but speculated sources include runoff from cow manure application sites,

wastewater from a slaughterhouse and meat packing plant, and municipal wastewater treatment
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plant effluent (Casman, 1996). Four documented cases of cryptosporidiosis occurring since 1984

have been linked to non-point source agricultural pollution (Mulla, 1999). Two outbreaks of

Cryptosporidium parvum were also traced to contamination of drinking water by cow manure in

England (Stehman, 2000).

The mandated treatment of public water supplies helps reduce the risk of infection via drinking

water, but the first step in providing safe drinking water is source water protection, especially

because Cryptosporidium parvum is resistant to conventional treatment.

Escherichia coli is an important cause of bacterial waterborne infection in untreated and

recreational water (Stehman, 2000). Infection can be life-threatening, especially in the young and

in the elderly. It can cause bloody diarrhea and, if not treated promptly, can result in kidney

failure and death (Shelton, 2000). In particular, Escherichia coli O157:H7 is emerging as the

second most important cause of bacterial waterborne disease after Shigella species, which is

associated with human feces. Escherichia coli O157:H7 was unknown until 1982, when it was

associated with a multistate outbreak of hemorrhagic colitis (Shelton, 2000). In 1999, an

Escherichia coli outbreak occurred at the Washington County Fair in New York State. This

outbreak was possibly the largest waterborne outbreak of Escherichia coli O157:H7 in U.S.

history. It took the lives of two fair attendees and sent 71 others to the hospital. An investigation

identified 781 persons with confirmed or suspected illness related to this outbreak. The outbreak

is thought to have been caused by contamination of the Fair’s Well 6 by either a dormitory septic

system or manure runoff from the nearby Youth Cattle Barn (NYSDOH, 2000). More recently,

in May 2000, an outbreak of Escherichia coli O157:H7 in Walkerton, Ontario resulted in at least

seven deaths and 1,000 cases of intestinal problems; public health officials theorize that one

possible cause was floodwaters washing manure contaminated with Escherichia coli into the

town’s drinking water well; an investigation is currently underway (Brooke, 2000). An outbreak

of Escherichia coli O157:H7 was reported in Canada from well water potentially contaminated

by manure runoff (Stehman, 2000).

Cow manure has specifically been implicated as a causative factor in the high bacteria levels and

ensuing swimming restrictions on Tainter Lake, Wisconsin (Behm, 1989). Contact recreation

can result in infections of the skin, eye, ear, nose, and throat (Juranek, 1995; Stehman, 2000). 

The EPA’s recommended ambient water quality standard for human health protection in contactrecreational fresh waters is either 120 Escherichia coli bacteria/100 ml, or 33 enterococcus

bacteria/100 ml. (This standard, finalized in 1986, replaces the previous standard of 200 fecal

coliform bacteria/100 ml.) About 8 percent of U.S. outbreaks of Escherichia coli O157:H7

between the years 1982 and 1996 occurred as a result of swimming (Griffin, 1998). Certain

regions, in particular, may be adversely impacted. For example, pathogen impairment of surface

waters is a great problem in most rural areas of southern Minnesota. This causes many rivers and

lakes to be unsuitable for swimming (Mulla, 1999). 

Most human infections caused by bacteria such as Escherichia coli O157:H7, Salmonella

species, Campylobacter jejuni, and Leptospira species are spread by foodborne or direct contact

(Stehman, 2000). Many pathogens might be transmitted through shellfish (Stelma and McCabe,
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1992), which are filter feeders prone to accumulating bacteria and viruses. Others may be

transmitted through inhalation. In particular, there is concern that pathogens may also be

introduced to the air directly from animal feeding houses or during spray application of wastes. 

Flies and other vectors also present potential pathways for disease transmission.

A final concern is exposure to pathogens via consumption of raw foods improperly subjected to

manure application. Cieslak et al. (1993) suggest that a 1993 Escherichia coli outbreak in Maine

was the result of manure applications to a vegetable garden. Additionally, three Escherichia coli

outbreaks (Montana in 1995, Illinois in 1996, and Connecticut in 1996) were traced to organic

lettuce growers. It is suspected that the lettuces were contaminated by infected cattle manure

(Nelson, 1997). In another incident in Maine, a few hundred children were sickened by

Cryptosporidium parvum. The source was fresh-pressed apple cider made from apples gathered

from a cattle pasture (Millard et al., 1994). Although this exposure route can cause health

problems, the proposed revisions to the EPA regulations do not attempt to address it directly.

3.4 ORGANIC MATTER

3.4.1 Ecology

Increased organic matter loading to surface waters supports increased microbial population and

activity; as these organisms aerobically degrade the organic matter, dissolved oxygen is

consumed, reducing the amount available for aquatic organisms. This impact is exacerbated in

warm waters compared to colder waters, because the dissolved oxygen saturation level is lower

and because the higher temperatures support increased microbial metabolism.

As a result of dissolved oxygen depletion, aquatic species may suffocate (USEPA, 1993a) or be

driven out of areas that lack sufficient oxygen. This phenomenon can occur rapidly, particularly

with loadings of high-strength waste such as those that may result from catastrophic lagoon

breaches (Goldman and Horne, 1983). There are many examples nationwide of fish kills

resulting from manure discharges from animal feeding operations (see Chapter 4). In Nebraska

in 1995, 50 percent of all agriculture-related fish kills investigated were due to livestock waste. 

In 1996, that percentage rose to 75 percent. In 1997 and 1998, 100 percent of agriculture-related

fish kills were traced to livestock waste (USFWS, 2000).

Oxygen-stressed aquatic systems may also experience decreases in species richness or

community structure as sensitive species are driven out or die off. Organisms living in

borderline hypoxic (low oxygen) water are also likely to experience physiological stress, which

may increase the potential for diseases, decrease feeding rates, or increase predation. Livestock

has been widely reported to cause significant decreases in wildlife species and numbers (Mulla et

al., 1999). For example, reduction in biodiversity due to AFOs has been documented in a study

of three Indiana stream systems (Hoosier Environmental Council, 1997). That study shows that

waters downstream of animal feedlots (mainly swine and dairy operations) contained fewer fish

and a limited number of species of fish in comparison with reference sites. Excessive algal
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growth; altered oxygen content; and increased levels of ammonia, turbidity, pH, and total

dissolved solids were also observed.

High oxygen depletion rates due to microbial activity have been reported in manure-amended

agricultural soils as well. In soils, elevated microbial populations can affect crop growth by

competing with plant roots for soil oxygen and nutrients (USDA, 1992).

3.4.2 Human Health

The release of organic matter to surface waters is a human health concern insofar as it can impact

drinking water sources and recreational waters. As aquatic bacteria and other microorganisms

degrade organic matter in manure, they consume dissolved oxygen. This can lead to foul odors

and ecological impacts, reducing the water’s value as a source of drinking water and recreation. 

Additionally, increased organic matter in drinking water sources can lead to excessive production

of harmful chlorinated byproducts, resulting in higher drinking water treatment costs and/or

higher health risks. Pathogen growth is another concern, as large inflows of nutrient-rich organic

matter, under the right environmental conditions, can cause rapid increases in microbial

populations.

3.5 SALTS AND TRACE ELEMENTS

3.5.1 Ecology

Salts in manure can impact the water and soil environment. In fresh waters, increasing salinity

can disrupt the balance of the ecosystem. Drinking water high in salt content was shown to

inhibit growth and cause slowed molting in mallard ducklings (IEC, 1993). On land, salts can

accumulate and become toxic to plants, and reduce crop yields. Salts can damage soil quality by

reducing permeability and deteriorating soil structure (Bloom, 1999).

Trace elements in manure can impact plants, aquatic organisms, and terrestrial organisms. While

many of the trace elements are essential nutrients at low concentrations, they can have significant

ecotoxicological effects at elevated concentrations. For example, metals such as zinc (a feed

additive) can accumulate in soil and become toxic to plants at high concentrations. Arsenic,

copper, and selenium are other feed additives that can produce aquatic and terrestrial toxicity at

elevated concentrations. Bottom feeding birds can be quite susceptible to metal toxicity because

they are attracted to shallow feedlot wastewater ponds and waters adjacent to feedlots. Metals

can remain in aquatic ecosystems for long periods of time because of adsorption to suspended or

bed sediments or uptake by aquatic biota.

Several of the trace elements in manure are regulated in treated municipal sewage sludge (but not

manure) by the Clean Water Act’s Part 503 Rule. Total concentrations of trace elements in

animal manures have been reported as comparable to those in some municipal sludges, with

typical values well below the maximum concentrations allowed by Part 503 for land-applied

sewage sludge (Sims, 1995). Based on this information, trace elements in agronomically applied
3-14

manures should pose little risk to human health and the environment. However, repeated

application of manures above agronomic rates could result in exceedances of the cumulative

metal loading rates established in Part 503, thereby potentially impacting human health and the

environment (USFWS, 1991).

In 1991, the U.S. Fish and Wildlife Service (USFWS) reported on suspected impacts from a large

number of cattle feedlots on Tierra Blanca Creek, upstream of the Buffalo Lake National

Wildlife Refuge in the Texas Panhandle. USFWS found elevated concentrations of the feed

additives copper and zinc in the creek sediment (as well as elevated aqueous concentrations of

ammonia, chemical oxygen demand, chlorophyll a, coliform bacteria, chloride, conductivity,

total Kjeldahl nitrogen, and volatile suspended solids). The relative contribution of these

contaminants from various sources (e.g., runoff from facilities without containment lagoons,

lagoon discharges, and lagoon leachate) was not assessed (USFWS, 1991).

In 1998, USFWS found copper and zinc in wetlands fed by wastewater from a nearby swine

production operation in Nebraska. Concentrations of copper exceeded both a proposed aquatic

life criterion of 43 μg/L and the current least-protective criterion of 121 μg/L. Zinc

concentrations exceeded the concentrations recommended for the protection of aquatic life

(USFWS, 2000).

3.5.2 Human Health

Salts from manure can impact surface and ground water drinking water sources. Salt load into

the Chino Basin from local dairies is over 1,500 tons per year, and the cost to remove that salt by

the drinking water treatment system ranges from $320 to $690 for every ton (USEPA, 1993b). 

At lower levels, salts can increase blood pressure in salt-sensitive individuals, increasing the risk

of stroke and heart attack. Salts can also make drinking water unpalatable and unsuitable for

human consumption. 

Some of the trace elements in manure are essential nutrients required for human physiology; 

however, they can induce toxicity at elevated concentrations. These include zinc, arsenic,

copper, and selenium, which are feed additives (Sims, 1995). Although these elements are

typically present in relatively low concentrations in manure, they are of concern because of their

ability to persist in the environment and to bioconcentrate in plant and animal tissues. These

elements could pose a hazard if manure is overapplied to land, due to insufficient acreage

available to accommodate manure from increasingly concentrated AFOs. Over-applied manure

increases the likelihood of pollutants reaching surface water and ultimately being ingested.

Trace elements are associated with a variety of illnesses. For example, arsenic is carcinogenic to

humans, based on evidence from human studies; some of these studies have found increased skin

cancer and mortality from multiple internal organ cancers in populations who consumed drinking

water with high levels of inorganic arsenic. Arsenic is also linked with non-cancer effects,

including hyperpigmentation and possible vascular complications. Selenium is associated with
3-15

liver dysfunction and loss of hair and nails, and zinc can result in changes in copper and iron

balances, particularly copper deficiency anemia (IRIS, 2000).

3.6 SOLIDS

Excessive silting and sedimentation are prime agents responsible for the long-term degradation

of rivers, streams, and lakes. Major sources of siltation include runoff from agricultural, urban,

and forest lands and other non-point sources (USEPA, 1992b). 

Solids entering surface water can degrade aquatic ecosystems to the point of non-viability. 

Suspended particles can reduce the depth to which sunlight can reach, decreasing photosynthetic

activity (and the resulting oxygen production) by plants and phytoplankton. The increased

turbidity also limits the growth of desirable aquatic plants that serve as critical habitat for fish,

crabs, and other aquatic organisms. In addition, suspended particles can clog fish gills, degrade

feeding areas, and reduce visibility for sight feeders (Abt Associates, 1993), and can disrupt

migration by interfering with fish’s ability to detect chemical communication signals in water

(Goldman and Horne, 1983). Sediment can smother eggs, interrupt the reproductive process, and

alter or destroy habitat for fish and benthic organisms.

Solids can also degrade drinking water sources, thereby increasing treatment costs. Furthermore,

solids provide a medium for the accumulation, transport, and storage of other pollutants,

including nutrients, pathogens, and trace elements. Sediment-bound pollutants often have a long

history of interaction with the water column through cycles of deposition, resuspension, and

redeposition.

3.7 ANTIBIOTICS AND ANTIBIOTIC RESISTANCE

Antibiotic-resistant strains of bacteria develop as a result of continual exposure to antibiotics. 

Use of antibiotics in raising animals, especially broad spectrum antibiotics, is increasing. As a

result, more strains of antibiotic-resistant pathogens are emerging, along with strains that are

increasingly resistant (Mulla, 1999). Antibiotic-resistant forms of Salmonella, Campylobacter,

Escherichia coli, and Listeria are known or suspected to exist. An antibiotic-resistant strain of

the bacterium Clostridium perfringens was detected in the ground water below plots of land

treated with swine manure, while it was nearly absent beneath unmanured plots.

Antibiotic resistance poses a significant health threat. In April 2000 the New England Journal of

Medicine published an article that discussed the case of a 12-year-old boy infected with a strain

of Salmonella that was resistant to no fewer than 13 antimicrobial agents (Fey et al., 2000). The

cause of the child’s illness is believed to be exposure to the cattle on his family’s Nebraska

ranch.

The Centers for Disease Control and Prevention, the Food and Drug Administration, and the

National Institutes of Health issued a draft action plan in June 2000 to address the increase in

antibiotic resistant diseases (CDCP, 2000). The plan is intended to combat antimicrobial
3-16

resistance through surveys, prevention and control activities, research, and product development.

One of the action items involves conducting pilot studies to assess the impact of environmental

contamination by antimicrobial drug residues and drug-resistant organisms that enter the soil or

water from human and animal waste.

3.8 HORMONES AND ENDOCRINE DISRUPTION

The presence of estrogen and estrogen-like compounds in surface water has caused much

concern. Their ultimate fate in the environment is unknown, although early studies indicate that

no common soil or fecal bacteria can metabolize estrogen (Shore et al., 1995). When present in

high concentrations, hormones in the environment are linked to reduced fertility, mutations, and

the death of fish, and there is evidence that fish in some streams are experiencing endocrine

disruption (Shore et al., 1995; Mulla, 1999).

Estradiol, an estrogen hormone, was found in runoff from a field receiving poultry litter at

concentrations up to 3.5 μg/L. Fish exposed to 0.25 μg/L of estradiol often have gender changes;

exposures at levels above 10 μg/L can be fatal (Mulla, 1999). Estrogen levels of 10 μg/L have

been shown to affect trout (Shore et al., 1995).

Endocrine disruptors have also been the subject of increasing concern because they alter hormone

pathways that regulate reproductive processes in both human and animal populations. Estrogen

hormones have been implicated in the drastic reduction in sperm counts among European and

North American men (Sharpe and Skakkebaek, 1993) and widespread reproductive disorders in a

variety of wildlife (Colburn et al., 1993). A number of agricultural chemicals have also been

demonstrated to cause endocrine disruption as well, including pesticides (Shore et al., 1995). 

The effects of these chemicals on the environment and their impacts on human health through

environmental exposures are not completely understood. They are currently being studied for

neurobiological, developmental, reproductive, and carcinogenic effects (Tetra Tech, 2000a). The

EPA is not aware of any studies done on the human health impact of hormones from watersheds

that have impairment from animal manure.

3.9 OTHER POLLUTANTS OF CONCERN

3.9.1 Gas Emissions

Odor sources include animal confinement buildings, waste lagoons, and land application sites. 

As animal waste decomposes, various gases are produced. The primary gases associated with

aerobic decomposition include carbon dioxide and ammonia. Gases associated with anaerobic

conditions, which dominate in typical, unaerated animal waste lagoons, include methane, carbon

dioxide, ammonia, hydrogen sulfide, and over 150 other odorous compounds (USDA, 1992;

Bouzaher et al., 1993; O’Neill and Phillips, 1992). These include volatile fatty acids, phenols,

mercaptans, aromatics, sulfides, and various esters, carbonyls, and amines. The decomposition

process is desirable because it reduces the biochemical oxygen demand and pathogen content of

the waste. However, many of the end products can produce negative impacts, including strong
3-17

odors. Heavy odors are the most common complaint from neighbors of swine operations in

particular (Agricultural Animal Waste Task Force, 1996).

Odor is itself a significant concern because of its documented effect on moods, such as increased

tension, depression, and fatigue (Schiffman et al., 1995). Odor also has the potential for vector

attraction and affects property values. Additionally, many of the odor-causing compounds can

cause physical health impacts. For example, hydrogen sulfide is toxic, and ammonia gas is a

nasal and respiratory irritant. 

In 1996, the Minnesota Department of Health found levels of hydrogen sulfide gas at residences

near AFOs that were high enough to cause symptoms such as headaches, nausea, vomiting, eye

irritation, respiratory problems (including shallow breathing and coughing), achy joints,

dizziness, fatigue, sore throats, swollen glands, tightness in the chest, irritability, insomnia, and

blackouts (Addis et al., 1999). In an Iowa study, neighbors within two miles of a 4,000-sow

swine facility reported more physical and mental health symptoms than a control group (Thu,

1998). These symptoms included chronic bronchitis, hyperactive airways, mucus membrane

irritation, headache, nausea, tension, anger, fatigue, and confusion.

Methane and carbon dioxide are greenhouse gases that contribute to global warming. Methane

also contributes to the formation of tropospheric ozone (a component of photochemical smog). 

Based on various EPA estimates (USEPA, 1989 and USEPA, 1992a), methane emissions from

U.S. animal wastes are a very small contributor to the global warming effect.

3.9.2 Particulates

Sources of particulate emissions from AFOs may include dried manure, feed, skin, hair, and

possibly bedding. The airborne particles make up an organic dust, which includes endotoxin (the

toxic protoplasm liberated when a microorganism dies and disintegrates), adsorbed gases, and

possibly steroids (Thu, 1995). At least 50 percent of dust emissions from swine production

facilities are believed to be respirable. The main impact downwind appears to be respiratory

irritation due to the inhalation of organic dusts. Studies indicate that the associated microbes

generally are not infectious, but may induce inflammation (Thu, 1995).

3.9.3 Pesticides

Pesticides may pose risks to the environment, such as chronic aquatic toxicity, and human health

effects, such as systemic toxicity. In a few studies, common herbicides have been shown to

cause endocrine disruption. There is some evidence that fish in some streams are experiencing

endocrine disruption and that contaminants including pesticides may be the cause (Mulla, 1999).
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