Resumo. Abstract: Aim This study aimed to evaluate the Trophic State Index (TSI) at the margin and in the channel of the Patos Lagoon estuary, considering different hydrological conditions. Methods Surface and bottom water samples were collected in three sites in the channel (margin and center) and in two sites at the Saco da Mangueira in different hydrological conditions in 2011. Results Waters at the Saco da Mangueira are very contaminated by phosphate and nitrogenous compounds. The TSI classifies these waters as being hypereutrophic, the consequence of both the release of effluents which were poorly treated and the low water flow in the inlet. Contamination was mild at the margins of the channel, where waters were classified as being eutrophic and mesotrophic. Trophic balance (mesotrophic waters - oligotrophic surface - bottom) was found in the center of the channel as a consequence of strong water flow and dilution of contaminants coming from the margins. Conclusions Spatial variation in the TSI value enabled clear distinction to be observed between the areas at the margins and in the channel, because it reflected the punctual presence of anthropogenic input in the marginal waters, mainly in the Saco da Mangueira. Effluent treatment must be required in order to control severe trophic imbalance in the waters at the margins of the city. Variations of the proposed index are a useful tool to identify sources of phosphate compounds in other aquatic environments.