Eutrophication is the most widespread effect of urban development in coastal areas. To elucidate how nutrient loading affects the carbon pathways at the base of food chains, we quantified the carbon transfer among microbial components, from prokaryotes to microzooplankton. For this purpose, we performed two size-fractionation feeding experiments during late summer under moderate (N: 28.5 μM, P: 0.92 μM, Si: 45.8 μM) and severe (N: 173.9 μM, P: 3.5 μM, Si: 67.2 μM) cultural eutrophication in the Bahía Blanca Estuary (Argentina). In both experiments, prokaryotes were largely dominated by heterotrophic forms, small diatoms dominated among autotrophs, and heterotrophic nanoflagellates were the most abundant among protistan grazers. Under severe eutrophication, however, the average biomass was 75% lower for all autotrophic and heterotrophic components. Nutrient loading sustained a higher growth rate of heterotrophic bacteria and phytoplankton but implied poorer trophic transfer. Under moderate eutrophication, daily productivity of nanoplankton and bacteria grazed was 157% and 154%, respectively, while under severe eutrophication, this percentage dropped to 3.54% and 33.7%, respectively. In addition, under excess nutrient conditions, microzooplankton evidenced an active prey switching toward the most abundant prey (diatoms). Weak top-down control of bacterial biomass along with trophic decoupling between microzooplankton and nanoflagellates, constituted a dead-end of bacterial biomass under severe cultural eutrophication. This inefficient carbon transfer can potentially produce a positive feedback by exacerbating organic matter accumulation.