http://www.newscientist.com/article/dn7046-hydroelectric-powers-dirty-secret-revealed.html
Hydroelectric dams produce significant amounts of carbon dioxide and methane, and in some cases produce more of these greenhouse gases than power plants running on fossil fuels. Carbon emissions vary from dam to dam, says Philip Fearnside from Brazil's National Institute for Research in the Amazon in Manaus. "But we do know that there are enough emissions to worry about."
In a study to be published in Mitigation and Adaptation Strategies for Global Change, Fearnside estimates that in 1990 the greenhouse effect of emissions from the Curuá-Una dam in Pará, Brazil, was more than three-and-a-half times what would have been produced by generating the same amount of electricity from oil.