Fluctuations in salinity may cause huge economic losses in estuaries with exploited commercial bivalves owing to their effect on mortality of these species. However, the same decrease in salinity does not affect all species in the same way, so it is interesting to study the effect of salinity from a multispecies standpoint. In the management of exploited bivalve beds, it is important to know the tolerance thresholds of the species, not only in cases of extremely low salinities but also over prolonged periods when salinities are low but not extreme. An analysis of mortality episodes of commercial bivalves in the Ulla River estuary (Galicia, NW Spain) from 1977 to 2009 revealed two mortality patterns related to how greatly the different species were affected. A mathematical model was designed to estimate salinity in the estuary based on weather conditions and tidal amplitude. By applying this model, it was possible to deduce the intensity and duration of the salinity decrease in the days prior to each mortality episode with the goal of relating these factors to mortality patterns. The two parameters found to be sufficient to explain the mortality observed were the minimum salinity at high tide and the number of consecutive days below a specific salinity threshold.