One infrequently discussed but very real issue with pumped storage is biogenic methane. In some cases, reservoirs can make more greenhouse gas per kWh than coal(!). Earlier we thought this was just bad in tropics but more recent studies indicate it may be most strongly correlated simply to reservoir size. If these are even moderately accurate, pumped storage for significant energy storage is not an option for a carbon-free system.

[1] http://pubs.acs.org/doi/abs/10.1021/es401820p

[2] http://journals.plos.org/plosone/article?id=10.1371/journal....