* most of the "good sites" have already been taken
* hydro will regularly silt up, requiring constant dredging
* hydro does not work as well or at all in drought conditions, which are increasingly common
* hydro dams require reservoirs, which in addition to the obvious disruption of the displacement of thousands or even a million plus people in the case of Three Gorges, can end up emitting large amounts of carbon as flooded vegetation decomposes.
* hydro is extremely disruptive to migratory fish. the success rate of interventions like fish ladders is in the low single digit percents. so you can get a bunch of carbon free power but also destroy an ecosystem in the process, not to mention any downstream fishing. and you see similar effects with other things that downstream users might want from the river like fresh silt.