Eelgrass is a species of seagrass that occurs widely in lagoons, estuaries, and coasts. Functioning of eelgrass bed communities are strongly affected by environmental factors such as salinity. Recently, salinity fluctuation is getting greater in coastal areas due to occurrence of more concentrated heavy rain which is related to the ongoing climate change. This change in disturbance regime (longer decline and more frequent fluctuation in salinity) can potentially change functioning and species interactions of eelgrass bed communities. The objectives for this study are to examine the ecological and physiological responses of the major functional groups (eelgrass, epiphytic algae and invertebrate grazer) in eelgrass beds, and to see how the interaction between the functional groups is altered by salinity fluctuation. We conducted a mesocosm experiment with four different salinity fluctuation treatments to simulate different disturbance situations. We found that survivorship of the grazers decreased with increasing duration and frequency of the disturbance event. The responses of eelgrass, epiphytic algae, grazers and their interactions varied among different salinity treatments. The results suggest the potential negative effects of more intense freshwater discharge on the functionality of the eelgrass bed communities such as primary/secondary productivities and their stabilities.