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University of Minnesota Extension

Reduce water quality issues from manure

Minnesotans know how precious clean surface and groundwater is to recreation and wildlife habitat in the state. Access to clean water is something that many take for granted, but protecting it from harm needs to be a top priority.

Pollution from towns and farms harm both surface and groundwater. Nitrogen, phosphorus, and pathogens are the most common water pollutants from manure on farms.


Nitrogen – in the form of nitrate – is of most concern in groundwater since that is where 3 out of 4 Minnesotans get their drinking water.

  • The nitrate threshold for safe drinking water is only 10 ppm. Above that level, infants may develop a condition that limits the supply of oxygen to the blood.
  • Nitrates that leave Minnesota through the Mississippi River add to the Gulf of Mexico dead zone. Added nitrates cause an excess of ocean plants and algae to grow.
  • When the plants and algae die, they are decomposed by bacteria that use up dissolved oxygen. This causes areas of low oxygen to form where ocean plants and animals cannot live.


Phosphorus is a major concern because it causes excessive plant and algae growth in lakes and rivers. This causes an oxygen-depleting reaction similar to what happens in the Gulf of Mexico dead zone.

Fish kills and loss of habitat are caused by the decreased oxygen content. Certain types of algae growth caused by phosphorus (called harmful algal blooms) can harm the health of humans and animals that come in contact with them.


Pathogens such as harmful bacteria and viruses in manure become an issue when they enter waterways and groundwater.

E. coli, Cryptosporidium, and Giardia are just a few pathogens that can cause serious health problems in people and animals that come in contact with contaminated water.

Tips to reduce water quality impacts of manure:

Though farms are not the only source of water contamination, farmers still have the responsibility to do their part in protecting water quality. These recommendations can help farmers manage manure to reduce the amount of pollutants leaving their farm or field.

  1. Manage runoff and leaching from stockpiled manure. Stacking solid manure on a concrete pad will reduce leaching of nutrients through the soil. Also, placing the stockpile in an open-sided shed, on a level surface, and above the seasonal high-water table will reduce runoff risk. A catch basin can also be placed nearby to hold any runoff before it reaches a waterway.
  2. Manage runoff and leaching from open lots. Catch basins and grass buffer strips can be used to hold and filter runoff from open lots before it reaches a waterway.
  3. Manage leaching from storage pits. Impermeable concrete, synthetic, or clay soil liners should be used in manure pits to keep nutrients from leaching downward. Pits should also be monitored closely and pumped before overflowing.
  4. Use clean-water diversion system. Berms, ditches, and gutters can be used to divert upslope and rain water from areas with manure so that it does not carry nutrients and pathogens to waterways.
  5. Use correct manure application techniques on fields. Apply nutrients only as needed in accordance with the University of Minnesota and Minnesota Pollution Control Agency’s guidelines. Whenever possible, incorporate manure into the soil to reduce risk of surface runoff. Do not apply on saturated or frozen soils as this will increase runoff.

Chryseis Modderman, Extension educator

Reviewed in 2020

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