Granted it's a reasonably new field of study but the latest result are indicating that hydro power is none too clean.
First off is the massive carbon footprint involved in building a dam in the first place.
All that hard-rock blasting and concrete creates a far far larger footprint than a coal strip mine ripping off the overburden.
Most rivers suitable for hydro-electric dams have a high gradient(fast flowing).
Putting in a dam creates an artificial lake.
Apparently that completely changes the water chemistry.
The lake then becomes a large source of methane through siltation and biological action.
Especially after 10 years of dam life.
Methane has a far greater effect on the ozone layer and global warming than co2.
Plus co2 can be produced but apparently that cycle is incredibly complex and needs far more study.
its possible that the co2 can be managed by the way the dam is operated and the type of pollutants (mainly agricultural) that flow into the water above the dam.
On top of that oxygen is stripped out of the flowing watershed completely changing the water chemistry.
A while ago the Obama administration was not willing to grant Canada's hydroelectric industry an exception to it's proposed dirty energy or high carbon impact bills.
Now we see why.
The Americans are starting to get the same research data in as we are.
In Canada, Quebec is fighting this research tooth and nail.
Quebec is now lobbying hard to cancel all scientific research into hydro-electric power in Canada.
After Charest's rant in Copenhagen about Alberta and the O&G business the last thing he needs is a bunch of research proving hydro power is as bad for the environment as dirty coal generation.