We investigated the spatial distribution of heterotrophic bacteria associated with different water masses in the northern East China Sea (ECS) in summer. The surface water masses were divided into the Changjiang Diluted Water (CDW) and high salinity water (HSW). In the CDW region, the concentrations of dissolved inorganic nitrogen (DIN) and chlorophyll-a (Chl-a), and micro Chl-a contribution were high; and bacterial abundance (BA) and ciliate abundance (CA) were also high. In the HSW region with relatively low DIN concentrations, Chl-a concentration and micro Chl-a contribution were low, but pico Chl-a contribution was increased compared to those in the CDW region. BA did not show any significant difference from the CDW region, but CA was decreased. BA showed a positive correlation with Chl-a concentration in the CDW region; however, it did not show a significant correlation with Chl-a concentration in the HSW region. The ratio of bacterial carbon biomass/phytoplankton carbon biomass was exponentially increased with a decrease in the Chl-a concentration. Compared to the past (1990-2000s), the surface phosphate concentrations and the size of dominant phytoplankton have recently decreased in the ECS. Considering this trend of nutrient decrease and miniaturization of the phytoplankton, our results indicate that changes in the strength of the oligotrophic water mass could alter the function of the microbial food web.