Fish habitats consist of clean water, meaning no pollution from man or from other environmental sources. Another important aspect of a fish habitat is the presence of sustenance, either in form of plant life or other fish.
Congress defined essential fish habitat for federally managed fish species as "those waters and substrate necessary to fish for spawning, breeding, feeding, or growth to maturity.
http://www.psmfc.org/efh/efh.html
The biggest concerns that affect fish habitats are caused by man, examples include overfishing, pollution and destruction of their natural habitat.
Overfishing - occurs when fishing activities reduce fish stocks below an acceptable level. This can occur in any body of water from a pond to the oceans.
http://en.wikipedia.org/wiki/Overfishing
Water pollution - the contamination of water bodies such as lakes, rivers, oceans, and groundwater caused by human activities, which can be harmful to organisms and plants that live in these water bodies. It occurs when pollutants are discharged directly into water bodies without treating it first.
http://en.wikipedia.org/wiki/Water_pollution
More info on Water Pollution here
Water pollution can be classified in several different categories, ranging from bacterial to chemical to any other substance that endangers the organisms living in that water. Pollution usually lead to mutations in the fish causing infertility or other defects that prevent successful mating and therefore population growth.
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