Multivariate analyses applied to Pleistocene bivalve assemblages from the Oga Peninsula (northern Japan) discriminate three distinct assemblages. The assemblages and their taphonomy were used to recognize environmental settings and changes. The Astarte–Cyclocardia–Glycymeris assemblage indicates shelf environment (below the storm wave base) where gravels and shells are transported from shallower settings. Supply of the exotic coarse sediment probably enabled epifaunal bivalves to inhabit the sea floor. The Glycymeris assemblage is characterized by dominance of G. yessoensis and represents current-swept shoreface environment (above the storm wave base). The Moerella assemblage is characterized by bivalves inhabiting bay to open-marine conditions and diverse deposit-feeders, indicating a moderately land-locked environment, such as an open bay or a bay mouth. Fine-grained substrata rich in organic matters in the bay were probably suitable for the deposit-feeders. Ordination also shows the assemblages along two environmental gradients, a bathymetrical one and the other related to open-marine and bay conditions. The environmental changes are explained mainly by glacio-eustatic sea-level changes and alternation of coastal geomorphology caused by local crustal movements. This study also suggests that fossil assemblages can be a powerful tool to reconstruct environments and depositional dynamics even in intensely bioturbated sedimentary facies.