Sediment from tilling leads to soil erosion and sediment build up. Sediment clouds the water, clogs the waterways, and prevents plants from photosynthesizing. Nutrients from fertilizers and manure contain nitrogen and phosphorus which promote algae growth. The water becomes cloudy, there is no photosynthesis, the algae die, and bacteria use oxygen to decompose the algae. Salinity of streams is affected when irrigation return flows carry salts into the stream.
Aquatic wildlife are sensitive to salinity levels and are severely affected when salt levels rise.
Some management techniques to stop soil erosion and the addition of sediment and toxic chemicals to streams include livestock exclusion, preventative farming practices, and streambank setback. Livestock exclusion is the fencing out of livestock from areas such as streambanks and streambeds to provide for recovery of water quality and habitat functions. This also eliminates direct pollutant loading from manure deposition in the stream. Preventing overgrazing can reduce runoff and the addition of sediment and chemicals to the water. Also, runoff can be reduced by alternative cropping systems.