Plankton carbon biomass and carbon fluxes (C-flux) were determined in order to understand how the microbial food web differs between a eutrophic coastal and a meso-oligotrophic offshore site in Lake Erie (Ohio, USA) during spring and summer 1993. Bacterial C-flux increased from the spring month (May) to the summers month (August) at both sites, and was more important at the coastal site. Excessive nutrient inputs at the coastal site correlated with a high biomass of large, colonial or filamentous phytoplankton, which were not readily grazed by zooplankton. Shifts in algal assemblage to large, filamentous forms during the summer caused zooplankton to graze more heavily on bacteria and protozoa and thus the bacterial C- flux became higher than algal C-flux. At the offshore site, bacterial biomass was greater than phytoplankton biomass, but zooplankton grazed preferentially on nanoplankton. Consequently, both algal and bacterial C-fluxes were similar at the offshore site during the summer. Phytoplankton occurred in more edible forms compared to the summer at both sited during the spring and thus zooplankton heavily grazed on algae. Algal C-flux was much greater than bacterial C-flux at both sites during the spring. This study suggests that the importance of the microbial C-flux may differ along a seasonal and trophic gradient. Microbial C-flux may also be related to algal and zooplankton community structure, especially in more productive systems.