Eelgrass (Zostera marina) forms extensive meadows (eelgrass bed) in coastal and estuarine environments. Various functional groups of primary producers and macroinvertebrates inhabit and support high productivity in eelgrass beds. The phenology of plant and animal communities are expected to vary among sites with different environmental conditions because each functional group has specific requirements to abiotic/biotic factors. We studied seasonal dynamics of eelgrass bed communities in two lagoons under contrasting environmental conditions by monthly field surveys. One lagoon is Akkeshi-ko with a steep salinity gradient and the spatial difference in daily salinity fluctuations. Another is Notoro-ko with no salinity gradient and spatial variation in fluctuation. We focused on four functional groups of plants (eelgrass, epiphytes, microphytobenthos, water-column phytoplankton) and macroinvertebrates including gastropods and crustaceans. We hypothesized that the functional groups with similar traits and in similar ambient environmental conditions would exhibit similar seasonal patterns in abundance (biomass) and community structures. Our results show differences in seasonality in the abundance patterns among groups and between lagoons. The peak biomass of primary producers from both lagoons is related to the availability of nutrients and proximity to the river months. The seasonal dynamics of macroinvertebrate biomass are group-specific, but their community structures are lagoon-specific.