Phytoplankton contribute a major proportion of the supply of organic materials available to benthic marine environments, in the form of sinking particulate organic matter (POM). The deposited phytoplankton fuels both the microbial food web and biogeochemical transformation in the bottom water and sediments. Despite their importance in determining the fate of the OM supply in benthic and pelagic habitats, little is known about the bacterial dynamics at the water-sediment interface in relation to the quality of phytoplankton-originated POM reaching sediment. The present study characterized the diversity and composition of the bacterial communities in the water phrase of sediment-core microcosms provided with a POM quality gradient obtained by mixing diatom and cyanobacterial slurries in varying proportion. While bacterial-alpha diversity was stable across the gradient, changes in beta-diversity along the gradient were mainly driven by the changes in relative abundance rather than by the replacement of dominant taxa, with more pronounced changes at finer taxonomic levels. Sediment bacteria played a minor role in structuring the overly-water bacterial communities across the POM gradient. Moreover, a large proportion of phylogenetically diverse taxa was enriched along the gradient with a high cyanobacterial supply of POM, whereas fewer taxa of phylogenetically closely related were enriched by the high diatom supply. Our results show that variability in the phytoplankton composition of POM reaching the bottom water can impact the community assembly of bacteria inhabiting the water-sediment interface, with important implication for the potential interactions between phytoplankton and bacteria in benthic environments.