Understanding the relative importance of multiple factors influencing spatio-temporal variations of productions by invertebrates is an important goal in coastal marine ecosystems. We studied multiple functional groups of invertebrates (i.e. grazers, predators, and suspension feeders) in eelgrass (Zostera marina) ecosystems along salinity gradients to 1) evaluate the relative importance of environmental (salinity and water temperature), spatial, and temporal factors and primary producer biomass on spatio-temporal variations in invertebrate biomass, a proxy for production, and to 2) compare the patterns between Akkeshi and Notoro, lagoons with and without a strong gradient respectively. Multiple regressions on distance matrices (MRM) followed by variation partitioning were used for the analyses. Grazer biomass was most affected by the spatial factor, followed by the temporal factor and biomass of epiphytic microalgae in Akkeshi but not in Notoro. Predator biomass was explained by water temperature in Notoro but not in Akkeshi. Suspension feeder biomass was most affected by the spatial factor and microphytobenthos biomass in Akkeshi and by eelgrass biomass in Notoro. We conclude that the relative importance of each factor varied among the functional groups and suggest the importance of the gradients and resource availability on the spatio-temporal variations of invertebrate productions in eelgrass ecosystems.