There are 550 plants in the Alps with more than 10 MW and 2900 GWh of annual output (Source: Alpine Convention). This kind of pressure severly impacts the ecological integrity of Alpine rivers and lakes.

 
Widespread river and stream diversion and the construction of large storage reservoirs destroy natural living spaces. Hydroelectric power plants constitute one of the most serious threats to natural river systems, interrupting migration passageways and causing frequent flooding that reduce benthos biomass.

Likewise, not all hydroelectric power can be considered ‘clean’ energy. For example, many hydroelectric installations in the Alps use cheap coal or nuclear sourced power to pump water up to the reservoir which in turn produces valuable peak-load electricity.