DONATE
DONATE

Fertilizer & Manure Harm to Biodiversity

Chemical fertilizers and manure leak nitrogen and phosphorus into the environment through a wide variety of routes.[1-3]

Nutrient pollution – the excess of nitrogen and phosphorus – is one of the key drivers of biodiversity loss. Animal agriculture is the primary source of nutrient pollution.[4]

Nutrient pollution in waterways leads to eutrophication which can then lead to algal blooms and eventually hypoxia or “dead zones” where almost all aquatic life is extinguished.

 

  1. See, Overview of Chemical Fertilizers [question: “How do chemical fertilizers get dispersed into the environment?”]
  2. See, The Manure Problem
  3. See, Animal Ag Water Pollution Sources
  4. See, Animal Ag’s Contributions to Water Pollution

Globally, pollution is considered the 3rd or 4th largest driver of biodiversity loss, responsible for ~15% of losses.[1-3]
Of the many types of pollution, nutrient pollution (excess nitrogen and phosphorus) is probably the largest factor, with pesticides the other major portion.[4]
Animal ag is the primary driver of nutrient pollution, due to chemical fertilizers on feed crops and concentrated manure.[5]
Nutrient pollution causes the eutrophication of waterways, degrades air quality through ammonia emissions, and generates the nitrogen cascade causing multiple negative consequences in air, water, and soil, and is a major threat to all life on earth.[6]
Due to the major impacts on waterways, freshwater species are most severely threatened.[7]

 

  1. Jaureguiberry, P., et al., (2022). The direct drivers of recent global anthropogenic biodiversity loss. Science advances, 8(45), eabm9982, [“We show that land/sea use change has been the dominant direct driver of recent biodiversity loss worldwide. Direct exploitation of natural resources ranks second and pollution third…” Abstract, Figure 1]
  2. IPBES (2019) Global assessment report of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services, Summary for Policymakers, Brondízio, E. S., et al., (eds). IPBES secretariat, Bonn, Germany, p. 12. [Note that the land use change category also includes sea use change. “The direct drivers of change in nature with the largest global impact have been (starting with those with most impact): changes in land and sea use; direct exploitation of organisms; climate change; pollution; and invasion of alien species.”]
  3. Kanter, D. et al., (2022) Science briefs on targets, goals and monitoring In support of the post-2020 global biodiversity framework negotiations. Secretariat of the Convention on Biological Diversity, p. 4. [“The IPBES Global Assessment (IPBES 2019) ranked pollution as one of the five main drivers of biodiversity loss, accounting for about 12%, 17% and 15% of biodiversity loss in terrestrial, freshwater and marine ecosystems.” Note: IPBES researchers estimates are based on a metastudy of 154 reports.]
  4. Kanter, D., et al., (2022), p. 4. [“Pollutants of concern affecting biodiversity and nature’s contributions to people include nutrients, pesticides, plastics, industrial chemicals, heavy metals, light and noise. We provide background below on why nutrient (nitrogen and phosphorus) and pesticide pollution are of particular concern and are the focus of this brief.”]
  5. See, Animal Ag’s Contributions to Water Pollution [question: What is the key takeaway regarding animal ag’s contributions to U.S. water pollution?]
  6. See, Size of the Nutrient Pollution Problem
  7. NatureServe (2023) Biodiversity in Focus: United States Edition, p. 11. [“As a group, species associated with fresh water, including amphibians, snails, mussels, crayfish, and many aquatic insects, have the highest percentage of at-risk species, highlighting the importance of  conservation strategies to protect freshwater.”]

 Pollution is understood to be the 2nd or 3rd largest threat to biodiversity in the U.S.[1,2]
 Nutrient pollution is considered the leading type of pollution.[3-5]
 For freshwater species, nutrient pollution is likely the primary threat.[6,7]
 Freshwater species have the highest share of at-risk species.[8,9]

 

  1. NatureServe (2023) Biodiversity in Focus: United States Edition. NatureServe: Arlington, VA, Figure 6, p. 16.
  2. World Wildlife Fund (2024) Living Planet Report 2024 – A System in Peril. WWF, Gland, Switzerland, Chart p. 29.
  3. Rosa L., et al., (2023) Biodiversity in Crisis: Exploring Threats to America’s Most Imperiled Species. Defenders of Wildlife, p. 5. [“Increased nutrient inputs from agricultural practices or atmospheric deposition is the leading type of pollution.” Note that large shares of atmospheric deposition are from agriculture.]
  4. See, Lakes, Rivers & Streams Pollution [question: “If biological condition is the key indicator, why focus on nutrient levels?”]
  5. Kanter, D., et al., (2022) Science briefs on targets, goals and monitoring In support of the post-2020 global biodiversity framework negotiations. Secretariat of the Convention on Biological Diversity, p. 4.
    [“Pollutants of concern affecting biodiversity and nature’s contributions to people include nutrients, pesticides, plastics, industrial chemicals, heavy metals, light and noise. We provide background below on why nutrient (nitrogen and phosphorus) and pesticide pollution are of particular concern and are the focus of this brief.”]
  6. Biodiversity in Focus: United States Edition, Figure 6, p. 16. [Report estimates that 69% of freshwater animals are impacted by pollution, the leading impact.]
  7. Sayer, C. A., et al., (2025). One-quarter of freshwater fauna threatened with extinction. Nature, 1-8. p. 140. [“Among freshwater decapods, fishes and odonates, 54% of threatened species are considered to be affected by pollution, 39% by dams and water extraction, 37% by land-use change and associated effects from agriculture (from subsistence to agro-industry scales, excluding aquaculture; note that the threats of pollution and agriculture are strongly linked), and 28% by invasive species and disease.”]
  8. Biodiversity in Focus: United States Edition, p. 11. [“As a group, species associated with fresh water, including amphibians, snails, mussels, crayfish, and many aquatic insects, have the highest percentage of at-risk species, highlighting the importance of conservation strategies to protect freshwater ecosystems.”]
  9. Stein, B. A., et al., (2018). Reversing America’s Wildlife Crisis: Securing the Future of Our Fish and Wildlife. Washington, DC: National Wildlife Federation, p. 3. [“America’s freshwater animals have been particularly hard hit and approximately 40 percent of the nation’s freshwater fish species are now rare or imperiled.”]

Broadly estimated, ~50% of all nutrient pollution comes from animal ag.[1]

About 75% of nutrient pollution comes from all agriculture.[2]

 

  1. See, Animal Ag’s Contributions to Water Pollution. [Page calculates animal ag’s share of nutrient pollution]
  2. See, Nutrient Pollution and Animal Ag Overview [question: “Is agriculture the main source of U.S. nutrient pollution?”]

 Less than half of U.S. freshwater bodies are in good biological condition.[1] Biological condition is the “presence, number, and diversity” of life, including fish, invertebrates, and other organisms.[2,3]
 Almost three-fourths of U.S. lakes are eutrophic.[4]
 Less than one-third of rivers and streams have healthy biological communities.[5]
 The 5-year average size of the Gulf of Mexico dead zone is ~4,300 square miles.[6]

Nutrient pollution is the leading cause of these widely degraded conditions.[7] Freshwater species face the most severe risks of extinction.[8]

 

  1. U.S. EPA (2024). National Water Quality Inventory: Report to Congress. EPA 841-R-23-001, p. 4.
  2. U.S. EPA (2023) National Rivers and Streams Assessment: The Third Collaborative Survey. EPA 841-R-22-004. [“The biology of a water body (the biological condition) can be characterized by the presence, number, and diversity of macroinvertebrates, fish, and other organisms.”]
  3. U.S. EPA (2021) National Coastal Condition Assessment, p. 16. [“Good sites (for biological condition) have a wide variety of species, more diversity, and fewer pollution-tolerant species than fair or poor sites.”] 
  4. U.S. EPA (2024) National Lakes Assessment: The Fourth Collaborative Survey of Lakes in the United States, EPA 841-R-24-006. Trophic State Indicator, Exhibits 8 and 9.
  5. U.S. EPA (2023) National Rivers and Streams Assessment 2018 – 2019 Key Findings. https://www.epa.gov/national-aquatic-resource-surveys/national-river-and-streams-assessment-2018-19-key-findings [“Less than one-third of our river and stream miles (28%) had healthy biological communities…”]
  6. NOAA (2024) Gulf of Mexico ‘dead zone’ larger than average, scientists find. https://www.noaa.gov/news-release/gulf-of-mexico-dead-zone-larger-than-average-scientists-find [This is more than twice the size of the 5-yr average goal agreed to in 2001 (1,930 sq. miles), set with a target date of 2015.]
  7. See, Size of the Nutrient Pollution Problem [question: “Is nutrient pollution the leading cause of U.S. water pollution?”]
  8. NatureServe. 2023. Biodiversity in Focus: United States Edition. NatureServe: Arlington, VA, p. 11. [“As a group, species associated with fresh water, including amphibians, snails, mussels, crayfish, and many aquatic insects, have the highest percentage of at-risk species, highlighting the importance of conservation strategies to protect freshwater ecosystems.”]

Ammonia (NH3, a nitrogen compound) is the most damaging air pollutant from animal ag.[1] The great majority of ammonia comes from animal ag, mostly from manure.[2] Ammonia is emitted from manure as soon as it is excreted and continues throughout storage and crop application.[3]

Once ammonia is formed, it is quickly and widely dispersed in the atmosphere and is then deposited in various forms in terrestrial ecosystems and in waterways.[4] Because adding nitrogen is an “on” switch for growth for many plants, the impacts on ecosystems are often dramatic.[5]

Most assessments of ammonia-generated air pollution analyze the impacts on human health, which are unusually damaging.[6] There are far fewer assessments of the impacts on biodiversity, even though the damage can be severe.[7] Very few generalized assessments can be made about biodiversity impacts, because the reactions can vary from species to species, and from ecosystem to ecosystem.

A report by the USDA notes that of 94 tree species studied, 51 responded negatively to nitrogen deposition.[8] A study of terrestrial nitrogen pollution by USDA and EPA scientists concludes that “Often, one small alteration within an ecosystem can lead to a cascade of responses that ultimately significantly changes some aspect or use of the system.”[9]

 

  1. Rotz, C. A., et al., (2014). Ammonia emission model for whole farm evaluation of dairy production systems. Journal of environmental quality, 43(4), 1143-1158, p. 1143. [“Gaseous emissions from animal agriculture have become an important issue in the United States and in many other countries. Emissions include greenhouse gases, volatile organic compounds, and specific toxic compounds, of which ammonia (NH3) is the most important.”]
  2. U.S. EPA (2024) 2020 NEI Supporting Data and Summaries – Data Queries for Sector Summaries. [Query: National/Ammonia NH3/Livestock Waste (49.2%), fertilizer application (33.5%), agricultural field burning (2.7%) of total (5,482,484 tons). Of the 36.2% due to crop production, we estimate at least half is from feed crops.]
  3. Rotz, C. A. (2004). Management to reduce nitrogen losses in animal production. Journal of animal science, 82 (suppl_13), E119-E137, Table 2. [“Up to half of the excreted nitrogen is lost from the housing facility…”]
  4. See, Animal Ag Air Pollution Overview
  5. Guthrie, S., et al., (2018). The impact of ammonia emissions from agriculture on biodiversity. RAND Corporation and The Royal Society, Cambridge, UK, p. 7. [“Common, fast-growing species adapted to high nutrient availability thrive in a nitrogen-rich environment and out-compete species which are more sensitive, smaller or rarer.”]
  6. See, Animal Ag Ammonia & PM2.5 [question: “What are the human health costs of PM2.5 from animal ag?”]
  7. Krupa, S. V. (2003). Effects of atmospheric ammonia (NH3) on terrestrial vegetation: a review. Environmental pollution, 124(2), 179-221, p. 212 [“Natural and semi-natural ecosystems, as well as forests must be expected to be severely at risk from the current amount of N deposition.”]
  8. Clark, C. M., et al., (2021). Air pollution effects on forests: A guide to species ecology, ecosystem services, and responses to nitrogen and sulfur deposition. Vol I. Trees. FS-1156, USDA Forest Service, p. vi. [“N deposition, along with S deposition is a major stressor to tree species because of its wide-ranging and multi-faceted impacts.”]
  9. Pardo, L. H., et al., (2015). Impacts of nitrogen pollution on terrestrial ecosystems of the United States. Air & Waste Management Assoc., p. 2.

Nutrient pollution leads to eutrophication which can then lead to harmful algae blooms (HABs). HABs decrease oxygen levels and kill native aquatic plants and animals due to toxins and loss of habitat.[1-3] Nutrient pollution is the central though not sole factor in the creation of HABs.[4]

Because industrial animal agriculture is the primary cause of nutrient pollution, it is therefore the central driver of HABs.[5] The EPA has been challenged over its ineffective strategy to manage HABs, though it is hamstrung by an inability to regulate agricultural pollution from non-point sources as well as the unwillingness of federal agencies to clearly identify agriculture, specifically animal ag, as the primary source.[6,7]

 

  1. Burkholder, J. M., et al., (2018). Food Web and Ecosystem Impacts of Harmful Algae. In Harmful Algal Blooms, John Wiley & Sons, Inc., ch. 7, p. p. 243. [“They disrupt ecosystem function by decreasing biodiversity and altering energy flow within food webs, and they also cause low oxygen stress and/or destroy important habitats such as submersed vegetation meadows.” For the many reports of animal mortality from HAB’s and associated toxins, see Table 7.1, pp. 246-257]
  2. Capel, P., et al. (2018) Agriculture – A River Runs Through It – the Connections between Agriculture and Water Quality, National Water-Quality Assessment Project, Circular 1433, U.S. Geological Survey, p. 40. [“Under the conditions caused by eutrophication, blue-green algae can perpetuate this negative cascade accumulation of events, helping change well-oxygenated, native aquatic ecosystems, which are more biodiverse but may be relatively unproductive, to a condition of higher productivity but relatively low species diversity.”]
  3. Anderson, D., et al., (2021). Marine harmful algal blooms (HABs) in the United States: History, current status and future trends. Harmful Algae, 102, 101975, p. 4. [“HABs also cause mortalities of fish and wildlife (e.g., seabirds, whales, dolphins, and other marine animals), typically as a result of the transfer of toxins through the food web or when aquatic toxins are ingested or transferred across gills.”]
  4. Glibert, P. M. & Burford, M. A. (2017). Globally changing nutrient loads and harmful algal blooms: recent advances, new paradigms, and continuing challenges. Oceanography, 30(1), 58-69. pp. 66-67.
    [“The global expansion of HABs is real and is a consequence of increasing nutrient loads to land, sea, and air and the many pathways by which these nutrients leach to fresh and marine waters.”]
  5. See, Animal Ag’s Contributions to Water Pollution. [Page calculates animal ag’s share of nutrient pollution.]
  6. U.S. EPA Office of Inspector General (2021). EPA Needs an Agencywide Strategic Action Plan to Address Harmful Algal Blooms, Report No. 21-E-0264, p. 4 [“Congress chose not to address nonpoint sources through a regulatory approach, but the CWA required states to develop nonpoint source-management plans and established an EPA grant program to address nonpoint source pollution.”]
  7. U.S. GAO (2022) Water Quality – Agencies Should Take More Actions to Manage Risks from Harmful Algal Blooms and Hypoxia Report to Congressional Requesters, p. 2. [The primary causes are commonly obscured in a brief listing of sources.]

High nutrient levels and the growth of algae can eventually lead to hypoxia – the depletion of oxygen in waterways. Without sufficient oxygen, aquatic life cannot survive. Hypoxic zones (aka dead zones) occur in both freshwater and marine systems. Dead zones form each summer in bays, lakes, and coastal areas across the country, with well-studied occurrences in Lake Erie, the Chesapeake Bay, and most famously the Gulf of Mexico.[1]

Like most problems stemming from high levels of nutrient pollution, industrial animal ag is the key driver of dead zones, caused primarily by factory farm manure and fertilizers on feed crops.[2]

The largest dead zone is in the Gulf of Mexico, which has a five-year average size of ~4,300 square miles, almost as large as the state of Connecticut.[3] This severely hypoxic zone is mostly caused by heavy nutrient discharges from chemical fertilizers and manure.[4,5]

We calculate that manure from factory farms and the share of chemical fertilizers specifically applied to crops used for feed together generate about half of the nutrient pollution to the Gulf of Mexico.[6]

 

  1. U.S. EPA (2025) Nutrient Pollution The Effects: Dead Zones and Harmful Algal Blooms. https://www.epa.gov/nutrientpollution/effects-dead-zones-and-harmful-algal-blooms (Accessed 3/21/25)
  2. See, Animal Ag’s Contributions to Water Pollution. [Page calculates animal ag’s share of nutrient pollution.]
  3. U.S. NOAA (2024) Gulf of Mexico ‘dead zone’ larger than average, scientists find.
    https://www.noaa.gov/news-release/gulf-of-mexico-dead-zone-larger-than-average-scientists-find [The 5-year average size is 4,298 sq. miles, more than twice the goal agreed to in 2001 (1,930 sq. miles), set with a target date of 2015.]
  4. Robertson, D. M. & Saad, D. A. (2021). Nitrogen and Phosphorus Sources and Delivery from the Mississippi/Atchafalaya River Basin: An Update Using 2012 SPARROW Models. Journal of the American Water Resources Association, 57(3), 406–429, p.416. [Note: for phosphorus sources, see, p. 416. For sources of both N & P, see Figure 5]
  5. Rabalais, N. N. & Turner, R. E. (2019). Gulf of Mexico hypoxia: Past, present, and future. Limnology and Oceanography Bulletin, 28(4), 117-124, p. 122. [“Reversing this progression of watershed and coastal water quality damage requires reducing the use of artificial fertilizers, mono- or dual-agriculture systems, intensified animal husbandry, insufficiently treated wastewater, and unnecessary consumption of fossil fuels… Restoring coastal water quality by decreasing nutrient loads of the Mississippi River watershed means, in large part, changing farming practices and facilitating natural mechanisms for N removal.”]
  6. See, Animal Ag’s Contributions to Water Pollution [question: “What does the USGS estimate as animal ag’s contribution?” This calculation is based on an evaluation of the USGS Robertson report.]

Drivers of Biodiversity Loss