Spatial pattern of biodiversity is affected by both geographical and environmental factors, yet the relative importance of these factors for shaping coastal community structures is variable and still remains unclear. In this study, we compared community structures of eelgrass-associated marine macroinvertebrates from various transitional water ecosystems in Eastern Hokkaido to see 1) if the observed patterns in diversity and correlatedness are derived from spatial or environmental factors, and 2) if the beta-diversity is influenced by the steepness of environmental gradients within ecosystem. The diversity and spatial correlatedness among the targeted communities were compared by db-RDA analysis followed by the variation partitioning to measure the relative contribution of environmental/geographical factors to the variation in community structures. The dissimilarity of community composition among stations within each ecosystem was then compared with the gradient indices representing steepness of the environmental gradient. The result indicates that environmental factors contributed more than spatial factors for determining the community structures. The steepness of the environmental gradient did not correlate with within-ecosystem dissimilarity index based on the presence/absence data, but that based on the abundance data. These suggest the strong influences of environmental filtering on shaping community structures of transitional water ecosystems.