Obviously they stop them from flowing freely. They turn rivers into lakes. They change sedimentation patterns, temperatures, and erosion patterns. They affect the life (plant and animal) in the rivers.
You could probably have come up with most of those impacts yourself.
Dams keep a lot of nutrients from flowing through to the river below because they retain much of the debris that would otherwise suppliment the water. This subsequently impacts the food web of the river below the dam. For more information, see the answer to this previously asked question on GreenAnswers at: http://greenanswers.com/q/216720/water-oceans-ice/dams-infrastructure/what-impact-do-dams-have-animal-life-around-river
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