The Jundiaí-Potengi Estuary (JPE), northeast of Brazil, suffers from intense degradation due to anthropogenic pollution from different sources, including several punctual treated and untreated domestic sewage discharges. To evaluate the estuary surface sediment quality near the outlet of a wastewater treatment plant (WWTP), five sampling points were selected. Four campaigns were performed on dry and rainy seasons of the years 2015 and 2016. The sediment samples were submitted to chronic ecotoxicological tests with Nitocra sp., and to metals, granulometry, and total organic matter analysis. The geochemical data were analyzed through enrichment indexes and, multivariate analysis, was performed integrating the ecotoxicological data. The sediment did not display toxicity to Nitocra sp. however, some metals’ concentration (Mn, Pb, Cu, Ni, and Cd) exceeded the limits established by Brazilian legislation. In general, the concentration of the analyzed metals doubled from rainy season to dry season. Considering our findings, we suggest quantifying other classes of contaminants and conducting studies on the bioavailability of metals in JPE, as well as using other organisms of different trophic levels in ecotoxicity tests.