Large-capacity generating systems require dams and reservoirs, which means massive flooding. Flooding:
destroys terrestrial ecosystems;
displaces local communities; (see CBC clips on the Cree's opposition to the James Bay Project, or the BBC article on the China's Three Gorges) and
releases harmful substances into the water; until flooding, these substance, including mercury, had been stored in the ground;
Dams alter waterways and fish habitats, change the migration routes of fish and other animals, and disrupt the natural flow of nutrients and sediment. This is less of a problem with small-capacity run-of-river hydroelectric systems, since they have no either a very small dam or none at all.
The construction of hydro plants and dams is fossil fuel-intensive and releases GHGs.
Areas flooded to create reservoirs, especially in shallow tropical areas, give off GHG from decaying plants killed by flooding.