From within, healthy fish habitat requires clean, cool water. The pH can not be too basic, or too acidic or the insect and fish eggs will not develop to hatch. As well, excess siltation, clouding up the water will eventually settle to the bottom and cover the unhatched eggs. If a stream has a healthy insect and fish population, then you know the area above, below and within that stream is healthy. Two hundred years of land and water use have resulted in over-widened, silt laden streams and rivers.
Land clearing leads to fast runoff during rain events, snow thaw and spring freshets.
Dams, acid rain, silt and other pollution also cause major losses to fresh water fish habitat. But, we have the ability to reverse some of these impacts. Many everyday activities harms fish habitat. Everytime you turn on a light, the electricity required may have come from a hydroelectric dam that is blocking fish migration, or a fossil fuel generator which is producing acid rain emissions that will settle on our rivers making the water too acidic to sustain life. Maybe the tomato on your plate came from a farm that has cut away all the trees from a stream bank to create more room to grow food.