Fish sometimes suffer from the high ammonia levels in water contaminated by manure. Over a longer period, bacteria consume available oxygen as the manure breaks down, and fish may suffocate. Nutrients in the manure also promote the growth of algae and aquatic vascular plants, which further deplete oxygen levels when they die and decompose. Streams bordered by shrubs and trees tend to be narrow and deep, whereas eroded streams become wider and shallower. Soil erosion adds to the sediment loading of streams and rivers and contributes substances that are attached to soil particles, such as nutrients, pesticides, and bacteria.
Some fish depend on specific habitats to spawn.
Sedimentation of cobble or gravel spawning beds can suffocate fish eggs and reduce spawning success. Removal of vegetation along streams can alter the physical shape and stability of channels, leading to habitat degradation and increased costs for stream channel maintenance and remediation. Case study Effect on walleye reproduction of rehabilitating Mink Creek, Manitoba Mink Creek is one of the tributary streams draining into Dauphin Lake, Man. A major cause of the decline was extensive channelization of the tributary streams to improve agricultural drainage and reduce spring flooding. The stream channels were straightened and uniformly graded, which resulted in a shorter spring runoff period and eliminated most of the pool and riffle habitats used by walleye for spawning and incubation.