Resumo. Abstract Aim: There are few studies dealing with the biogeochemical processes occurring in small estuaries receiving high sewage loading in tropical regions. The aim of this investigation was to characterize the biogeochemical behavior of nutrients in superficial waters collected at the Iguaçu estuarine system, during specific conditions (neap tide), located at the inner sector of a heavily eutrophicated embayment (Guanabara Bay, SE Brazil). Methods Physical and chemical variables were measured in situ (pH, temperature, conductivity, salinity, total dissolved solids, transparency, dissolved oxygen), whereas suspended particulate matter, chlorophyll a, phaepigments and nutrients (carbon, nitrogen and phosphorus forms) were measured in laboratory across the mesohaline estuarine gradient. Results The Iguaçu River mouth is in a high stage of eutrophication, considering nutrient concentrations, chlorophyll a and transparency of water column. Results indicate a transition from heterotrophic conditions to autotrophic conditions, since the nutrients concentrations showed a decreasing pattern along the saline gradient, while the chlorophyll an increased over the transects. The pH values and chlorophyll : phaeopigments ratios are significantly related to the amount and quality of organic matter contents, especially at transects under strong marine influence. More than 95% of the dissolved and total nitrogen concentrations are represented by NH4+ contributions, which are related to the ammonification of organic matter contents in this region, indicating the existence of untreated sewage loads in this area. Conclusion In this study, the Iguaçu River seemed to contribute with high inputs of nutrients that support important phytoplankton production at the inner regions of the bay related to the CO2 sink and autotrophic metabolism, showing the importance of verifying the biogeochemical behaviors of nutrients in estuarine areas, even in small scale.