Habitat loss. Fish, frogs, birds, and insects all need the right type of vegetation in and beside the creek, to provide food, shelter, and shade, which keeps the water cool.
Pollution from roads and lawns. This type of pollution, called "non-point-source pollution", is hard to control because there's no single source. Oil from roadways and pesticides from lawns are terrible for creeks.
Culverts and channels. Concrete channels and underground culverts don't just look ugly, they also prevent natural creek processes like the growth of aquatic vegetation and the formation of pools and riffles. They also contribute to erosion and flooding, by forcing large volumes of water into constricted channels. Natural streams need to "meander" to alleviate flood pulses; channels and culverts eliminate those natural curves and detours.
Rapid runoff during storms. Vegetation and exposed ground have been replaced by parking lots and houses. These impermeable surfaces send runoff into creeks all at once, so water levels rise very high during storms and then drop quickly to low levels. The high levels cause erosion and destroy habitat; the low levels are too low to sustain creekside vegetation and create good pools for fish.
Dogs, feral cats, and people all cause problems. Dogs and cats sometimes eat eggs or young birds; people trample plants and track in non-native seeds; and everyone can scare birds off their nests, and disrupt their feeding patterns.
Non-native species disrupt the ecological balance. Invasive weeds can turn a complex ecosystem into a monoculture with little habitat value for native species; non-native animals and fish can displace natives. Click here for information on riparian habitat.