Here's an article that suggests that hydroelectric power isn't as green as it's cracked up to be. Why?
This is because large amounts of carbon tied up in trees and other plants are released when the reservoir is initially flooded and the plants rot. Then after this first pulse of decay, plant matter settling on the reservoir's bottom decomposes without oxygen, resulting in a build-up of dissolved methane. This is released into the atmosphere when water passes through the dam's turbines.
...In effect man-made reservoirs convert carbon dioxide in the atmosphere into methane. This is significant because methane's effect on global warming is 21 times stronger than carbon dioxide's.