Don't think hydro is a non-invasive type of power generation when it comes to the environment. It changes the whole river system it is on, affects migration and breeding of some fish many many impacts that cant be denied. Although I do belive wind hydro are mostly green as they don't pollute in the traditional sense, but they do affect the environment. There will be trade-offs in anything we do.
Environmental impacts were much more important in the 70's when it comes to hydroelectricity. That is because the main concern is the mercury released when inundating huge territories of forrest, which would poison the ecosystem for up to 30 years if I remember correctly. Nowadays Hydro-Quebec cuts all the wood beforehand.
In terms of disturbing the ecosystem, this is very temporary. It adapts quite quickly and just a trip to a site would convince you. I regularly go to the 'Baie James' (incredible trip for people who like fishing, hunting and sightseeing btw) and the ecosystem is just awesome.
You also have to think that the advantage of hydro-electricity isn't in it's cleanliness; wind and solar is much better in that regard. But it is in the fact that it acts as a lever to permit you to massively use those other types of none-reliable clean energies. This is because a water turbine takes 5 minutes to get up and running and producing energy, so makes a very easily reactive system to any unpredicted losses of wind, or bursts of energy demands in the middle of the night. (contrary to coal plants who takes days to get up and running I believe)
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