Hydrological alterations in watersheds have changed the flows of freshwater to many nearshore marine environments. The ensuing alterations to the salinity environment of coastal waters may have implications for species distribution. This study describes the response of two common bivalves to a modified salinity environment imposed by freshwater inputs from a hydroelectric power station in Doubtful Sound, New Zealand. Populations of Austrovenus stutchburyi and Paphies australis inhabiting river deltas near the outflow of the power station in inner Doubtful Sound were more than an order of magnitude smaller in abundance than populations in neighbouring Bradshaw Sound where the salinity regime is unaltered. In addition, there was a lack of small size classes of both species in inner Doubtful Sound, suggesting that these populations are unsustainable over the long term (10–20 years). Laboratory experiments demonstrated that sustained exposure (>30 days) to low salinity (