Pathogens are micro-organisms which can cause harm to human health and the environment. Pathogens include viruses, bacteria (such as E. coli and Salmonella), and protozoan parasites (such as Cryptosporidium and Giardia). Water-borne pathogens survive, and some reproduce, in water. Common sources of pathogens to aquatic ecosystems include municipal wastewater effluents, agricultural wastes (mainly livestock and poultry fecal waste), and wildlife. Surface water has a higher contamination risk than groundwater as the contaminants from the source will generally run off into the surface water before it infiltrates to groundwater.

Water-borne pathogens can be very harmful to humans, and affect health through drinking water, and fruits and vegetables that come into contact with surface water through irrigation or washing. The effect of a pathogen on humans depends on the type of pathogen and the concentration. For example, a pathogenic strand of E. coli, O157:H7, can cause illness in humans with the ingestion of fewer than 10 cells. It is estimated that 90,000 illnesses and 90 deaths a year in Canada are a result of water-borne pathogen infections. High pathogen levels in an aquatic system can also disturb human recreational activities like swimming as well as posing a threat to animal health, aquaculture and aquatic systems biodiversity.

Water used for irrigation and washing is regulated to reduce the risk of pathogenic contamination of food and run off to the environment. The Canadian Guidelines for Water Quality in Agricultural Uses states that irrigation water must have less than 100 fecal coliforms/ E.coli or 1000 total coliforms in 100 ml of water; drinking water standards, which is applied to wash water, is stricter with 0 total coliforms allowed in 100 ml. Many water-borne pathogens will decrease in the environment if no additional contaminated source water is added with the length of survival depending on individual micro-organism.

Nitrogen is an essential nutrient for the survival and growth of most living organisms.  Nitrogen gas is a large constituent of the atmosphere, making up approximately 80% of the air, but this form is inaccessible by most plants. Certain bacteria in soils have the ability to ‘fix’ naturally-occurring nitrogen from the atmosphere, which converts it to a usable form for the plants, it can also be fixed by lightning or through an industrial process which makes nitrogen fertilizers. Nitrogen is generally the limiting nutrient in terrestrial ecosystems, and is applied to fields through use of fertilizers and manure. Once in the soil, the nitrogen will be used by the crops, leached down, or emitted into the atmosphere. In the soil, ammonium (NH4+) or ammonia (NH3) is broken down by bacteria through nitrification in which it is converted first to nitrite and then to nitrate. 

Both nitrites (NO2-) and nitrates (NO3-) are highly soluble forms of nitrogen and thus are transported easily in water and do not attach to the soil. Nitrite is more toxic than nitrate but since the processes changing nitrite to nitrate happen quickly it is not generally found in large quantities. Though less toxic, high concentrations of nitrate in aquatic systems can have both acute and chronic lethal effects on amphibians as well as any species which prey on amphibians, such as fish. NH3 which has not been converted through nitrification can also have harmful effects on aquatic organisms. The major sources of NH3 in aquatic systems are wastewater and treatment plants.