Please do NOT pick up rocks
A rock is just a rock, right? It may be, except when it's a home. Rocks in streams move on their own during huge floods, but most often they move when people pick them up to search for critters underneath, or form a channel for tubing. No matter how the rocks move, the disturbance can harm the very creatures we value in our streams, including mayflies, caddisflies, salamanders, and fish. Many aquatic macroinvertebrates such as insects, snails, and crayfish use the cracks and undersides of rocks as sheltered homes. Park fisheries biologists also know that some endangered fish lay their eggs under rocks, which provide cover for the parents and protect the eggs. When people move rocks, adult fish flee and predators can find and eat all of the eggs.
It's very easy to avoid picking up rocks—just don't do it! Park biologists and entomologists who regularly study water quality, fish, and invertebrates in streams actually avoid going into the water during the egg-laying time for the endangered fish. If you're in a river, consider the critters that live under each rock and leave the roof on their homes. Choose bigger rivers where you don't have to move rocks into a channel to have fun, or enjoy a lazy float between rocks, knowing that you're keeping a river healthy.
The Environmental Protection Agency lists siltation as a major threat to water quality, and one that's increasing as construction on land near rivers removes the soil-holding-groundcover. Fine sediment fills gaps between rocks and sand grains (what we call interstitial spaces) that provide habitat for many organisms. It can also clog gills, making it hard for a fish, amphibian, or mayfly larva to breathe.