In shallow coastal areas, salinity fluctuation and sediment reworking due to wave action are two major stressors. Together these stressors can affect the ecological performances of the soft bottom organisms through affecting their energy metabolism and bioenergetics. In this data set, we estimated the energy reserves (protein, lipid and carbohydrate) and ETS capacity in soft shell clam, Mya arenaria under different salinity regime (5 psu, 15 psu and daily salinity cycle between 5 and 15 psu), exercise group (resting, burrowing and exhausted) and the interaction of salinity and exercise group.