The aim of this study was to evaluate the influence of shrimp farming on the phytoplankton community of a nearby shrimp estuary in Northeastern Brazil during a single cultivation cycle. Samples were collected from shrimp ponds and the estuary to analyse water quality variables, ecological indices and phytoplankton assemblages in both areas. Significant differences between sampling sites and over time were found for all variables. Phytoplankton density, orthophosphate and chlorophyll a content were lower in the estuary than in the ponds and were in accordance with Brazilian environmental law. Cyanophyta was abundant in the estuary and dominant in the shrimp ponds. Moreover, a significant positive correlation was found between Cyanophyta and orthophosphate. Thus, the influence of shrimp farming on the phytoplankton community was minimal or nil in the nearby estuary, as lower cell densities, a lower quantity of nutrients (especially orthophosphate) and better ecological health were found in the estuary than in the shrimp farm ponds. These findings contribute to a better understanding of the ecological balance in water bodies adjacent to aquaculture areas. Further studies should address the influence of wastewater from other aquaculture activities on the equilibrium of aquatic ecosystems.