Sampling was conducted monthly during a transition period between the dry and rainy seasons in order to evaluate the effectiveness of a municipal sewage treatment plant (STP) in eutrophication control. STP effluent and fluvial input data were also estimated. In the dry period, high concentrations of nutrients, chlorophyll a (up to 360 μg L(-1)), and anoxia in bottom waters were observed in the upper portion of the estuary. Nitrate was scarce during the dry months, although high concentrations were observed at the river sources and the upper estuary. The N:P and Si:P molar ratios were usually below 16:1, and the Si:N ratio was higher than 1:1. The fluvial inputs were a greater source of nutrients to the estuary than the STP, but nutrient loading by these effluents were also important in contributing to the eutrophication of the upper estuarine zone, especially in the dry season when symptoms were more intense.