Rivers possess a delicate ecology that depends on a regular cycle of disturbance within certain tolerances. The plant and animal communities that inhabit the river and river margins have evolved to adapt to their river's own peculiar pattern of flood and drought, slow and fast current. Dams disrupt this ecology. There are several types of dams.
The first effect of a dam is to alter the pattern of disturbances on which the plants and animals of a river depend. As an example, a fish on a certain river may only reproduce during April of every year so that its offspring will have abundant food and places to hide. If the normal spring flood never comes because a dam holds the river back, the offspring will be produced during a time when they cannot possibly survive. Vegetation, too, depends upon these regular cycles of flood. Quite often, people will decide that they can spare no water at all and no flooding at all will occur in the stream. Or they may have built the dams specifically to stop flooding so they can build houses in the floodplains. When this happens, riparian vegetation, the vegetation bordering the river, changes forever. An example of this may be found in much of the Southwest United States, where enormous floodplains of cottonwood, marsh and grasses have been replaced by dry, barren areas of tamarisk.
If the dam is allowed to release water from its reservoir, it will often do so only once in awhile, rather than in the frequent, small floods as are seen in nature. This leads to scouring and armoring of the riverbed. The higher energy of the sudden floods picks up and removes smaller sediments like silt, sand, and gravel, as well as aquatic plants and animals, leafy debris, and large woody debris. Complex sets of habitats are erased. The riverbed below the dam becomes like a pavement of cobbles and loses its value as habitat for plants, macroinvertebrates, and fish. Another reason that riverbeds become scoured and armored is that dams remove sediment from the river. The river, which now has no sediment, has improved carrying capacity and will pick up sediment from the streambed below the dam. It is much as though the river has been "starved" of its sediment. As in everything else in nature, balance will be achieved one way or the other.
Dams hold back not only sediment, but also debris. The life of organisms (including fish) downstream depends on the constant feeding of the river with debris. This debris includes leaves, twigs, branches, and whole trees, as well as the organic remains of dead animals. Debris not only provides food, it provides hiding places for all sizes of animals and surfaces for phytoplankton and microorganisms to grow. Without flooding and without a healthy riparian zone, this debris will be scarce. Adding to the problem, although debris might come from the river above the dam, it is instead trapped in the reservoir, and never appears downstream. The bottom level of the food web is removed. All in all, the loss of sediment and debris means the loss of both nutrients and habitat for most animals.
Temperature is another problem. Rivers tend to be fairly homogenous in temperature. Reservoirs, on the other hand, are layered. They are warm at the top and cold at the bottom. If water is released downstream, it is usually released from the bottom of the dam, which means the water in the river is now colder than it should be. Many macroinvertebrates depend on a regular cycle of temperatures throughout the year. When we change that, we compromise their survival. For instance, a stonefly may feel the cold temperatures and delay its metamorphosis. This may mean that at a critical lifestage it will be living in the depth of winter rather than in autumn as it should have been.
Fish passage is a concern with dams. Many fishes must move upstream and downstream to complete their lifecycles. Dams are often built without fish ladders. When fish ladders are provided, they seldom work as needed. If enough adult fishes do manage to climb above a dam, there remains the issue of their young: how will they get back downstream? Many are killed by predators while they wander in the slow waters of the reservoir above the dam. Many are killed in their fall downward through the dam to the river below. They aren't killed by the fall itself, but by the high levels of nitrogen gas at the base of the dam. In other words, like divers who go too deep, they get the "bends.