Extreme climate events, such as heatwaves and torrential rain, affect the physiology and functioning of marine species, especially in estuarine habitats, producing severe ecological and socioeconomic impacts when the affected species support important fisheries, such as artisanal shellfisheries. Studies of the impact of sudden decreases in salinity and increases in temperature were reviewed with the aim of producing comprehensive conceptual maps to aid the management of fisheries of the native clams Ruditapes decussatus and Venerupis corrugata, the introduced Ruditapes philippinarum, and the cockle Cerastoderma edule in Galicia (NW Spain). The maps show the effects on mortality, scope for growth, ability to burrow, changes in gonad development or predation risk. While V. corrugata will generally be more affected by low salinity (5 to 15) or high temperature (30 °C) during only two tidal cycles, C. edule populations may recover. Both species are also expected to become more vulnerable to predators. The clams R. philippinarum and R. decussatus will be more resistant, unless extreme events occur after massive spawning episodes; however, the presence of the intertidal seagrass Zostera noltei may buffer the negative effects of high sediment temperature on the growth of some species, such as R. decussatus. Finally, recommendations for assessing climate risk and designing management actions for shellfisheries are given.