Earlier quoted context omitted.
The biggest real problem with hydro is proper assessment of impact of local climate change and damage on ecosystems. You can find some readings about the effects of big hydropower projects in Siberia or Middle Asia. In the latter construction of hydropower plant may even become a casus belli due to deficite of water and impact on agriculture of the countries down the river.
I think that has more to do with the diversion of water for irrigation. For example, the almost-total vanishing of the Aral Sea.
There's also the Shuren Dam project which may damage ecosystem of Baikal.