Sedimentation
Sedimentation occurs when wind or water runoff carries soil particles from an area, such as a farm field, and transports them to a water body, such as a stream or lake. Excessive sedimentation clouds the water, which reduces the amount sunlight reaching aquatic plants; covers fish spawning areas and food supplies; and clogs the gills of fish. In addition, other pollutants like phosphorus, pathogens, and heavy metals are often attached to the soil particles and wind up in the water bodies with the sediment. Farmers and ranchers can reduce erosion and sedimentation 20 to 90 percent by applying management measures to control the volume and flow rate of runoff water, keep the soil in place and reduce soil transport.

Nutrients
Nutrients such as phosphorus, nitrogen and potassium in the form of fertilizers, manure, sludge, irrigation water, legumes and crop residues are applied to enhance production. When they are applied in excess of plant needs, nutrients can wash into aquatic ecosystems where they can cause excessive plant growth, which reduces swimming and boating opportunities, creates a foul taste and odor in drinking water, and kills fish. Nutrient management plans can help maintain high yields and save money on the use of fertilizers while reducing NPS pollution.

Improper Animal Waste Management
By confining animals to areas or lots, farmers and ranchers can efficiently feed and maintain livestock. But these confined areas become major sources of animal waste. Runoff from poorly managed facilities can carry pathogens (bacteria and viruses), nutrients, and oxygen-demanding substances that create major water quality problems. Ground water can also be contaminated by seepage. Discharges can be limited by storing and managing facility wastewater and runoff with an appropriate waste management system.

Inefficient Irrigation Systems
Inefficient irrigation can cause water quality problems. In arid areas, for example, where rainwater does not carry residues deep into the soil, excessive irrigation can concentrate pesticides, nutrients, disease-carrying microorganisms, and salts - all of which impact efficiency. Actual crop needs can be measured with a variety of equipment.

Pesticide
Pesticides, herbicides, and fungicides are used to kill pests and control the growth of weeds and fungi. These chemicals can enter and contaminate water through direct application, runoff and wind transport. They can kill fish and wildlife, poison food sources, and destroy animal habitat. Integrated Pest Management (IPM) techniques based on the specific soils, climate, pest history, and crop for a particular field can limit pesticide use and manage necessary applications to minimize pesticide movement from the field.

Overgrazing
Overgrazing exposes soils, increases erosion, encourages invasion by undesirable plants, destroys fish habitat, and reduces the filtration of sediment necessary for building stream banks, wet meadows, and floodplains. To reduce the impacts of grazing on water quality, farmers and ranchers can adjust grazing intensity, keep livestock out of sensitive areas, provide alternative sources of water and shade, and re-vegetate rangeland and pastureland.