During February 1998, a 100-year return flood occurred in the River Kerry, north-western Scotland. A study was undertaken in order to assess the impact of this event on a large, internationally important freshwater pearl mussel ( Margaritifera margaritifera L.) population. A conservative estimate of 50,000 mussels killed by the flood was made. This represents 4–8% of the total population. Significant channel reformation and large-scale movements of substrata occurred in some reaches, whereas others appeared to be unchanged. Some mussel beds disappeared or were largely depleted whereas others remained intact. Boulder-dominated substrata appear to have provided the most protection from scouring. The relatively high mussel densities and recruitment levels found in the middle reaches are probably due to the fact that this part of the river is hydrologically stable. It is likely that the intact mussel beds in the middle reaches will be the main source of regeneration in other parts of the river as the population recovers. As a result of recent changes in the hydrological behaviour of Scottish rivers, several M. margaritifera populations may now be more at risk from these catastrophic events. Therefore, it is important that conservation managers are aware of this potential threat.