Quantifying biotic feedbacks in response to environmental signals is fundamental to assess ecosystem perturbation. We analyzed the joint effects of eutrophication, derived from sewage pollution, and climate at the base of the pelagic food web in the Bahía Blanca Estuary (SW Atlantic Ocean). A two-year survey of environmental conditions and microplankton communities was conducted in two sites affected by contrasting anthropogenic eutrophication conditions. Under severe eutrophication, we found higher phytoplankton abundance consistently dominated by smaller sized, non siliceous species, while microzooplankton abundance remained lower and nutrient stoichiometry showed conspicuous deviations from the Redfield ratio. Phytoplankton growth in such conditions appeared controlled by phosphorous. In turn, microplankton biomass and phytoplankton size ratio (20μm) displayed a saturation relationship with nutrients in the highly eutrophic area, although mean phytoplankton growth was similar in both eutrophic systems. The strength of links within the estuarine network, quantified through path analysis, showed enhanced relationships under larger anthropogenic eutrophication, which fostered the climate influence on microplankton communities. Our results show conspicuous effects of severe sewage pollution on the ecological stoichiometry, i.e., N and P excess with respect to Si, altering nutrient ratios for microplankton communities. This warns on wide consequences on food web dynamics and ultimately in ecosystem assets of coastal pelagic environments.