Reservoirs located in urban areas suffer specific pressures related to human activities. Their monitoring, management, and protection requirements differ from reservoirs situated in non-urbanized areas. The objectives of this study were: (a) to determine the concentrations of select pesticides and emerging pollutants (EPs) present in an urban reservoir; (b) to describe their possible spatial distributions; and (c) to quantify the risks for aquatic life and safeguard drinking water supplies. For this purpose, the Guarapiranga reservoir was studied as an example of a multi-stressed urban reservoir in a tropical region. A total of 31 organic compounds (including pesticides, illicit drugs, pharmaceuticals, and endocrine disruptors) were analyzed twice over a period of one year, together with classical indicators of water quality. The physical and chemical data were treated using principal component analysis (PCA) to identify possible temporal or spatial patterns. Risk assessment was performed for biota and drinking water use, comparing maximum environmental concentrations (MECs) with the predicted no-effect concentrations (PNECs) or drinking water quality criteria (DWC), respectively. The results demonstrated the presence of pesticides and EPs, as well as pollution by high levels of nutrients and Chlorophyll a (Chl. a), during the study period. The nutrients and Trophic State Index (TSI) showed gradients in the reservoir and regional distributions, while the pesticides and EPs only clearly showed this pattern in the dry season. The concentrations and distributions of the pesticides and EPs therefore showed seasonality. These findings suggested that the two groups of pollutants (EPs+pesticides and nutrients) possessed different sources and behavior and were not always correlated in the reservoir studied. In the studied period, no risk was observed in raw water for drinking water use, but carbendazim, imidacloprid, and BPA showed risks for the biota in the reservoir.