Accumulation of pesticides has a harmful impact on the environment and human health. The main goal of this work was to develop a method to determine and quantify the residues of thirteen pesticides in edible fish and bivalves such as parati (Mugil curema), seabass (Centropomus ssp.), mullet (Mugil brasiliensis), clams (Anomalocardia brasiliana) and mussel (Mytilus galloprovincialis) collected from Sepetiba Bay and Parnaiba River Delta (Brazil) between 2019 and 2020. Matrix solid-phase dispersion (MSPD) was used for extraction and quantification through gas chromatography coupled to tandem mass spectrometry (GC-MS/MS). The method was validated (linearity, accuracy and precision) for fatty fish (Salmo salar), lean fish (Mugil curema) and bivalves (Mytilus edulis). The survey found linear correlation coefficients (r) equal to or greater than 0.9 for almost all analytes. The relative standard deviations (RSD) of five replicates were less than 20% for almost all analytes at different concentrations in lean fish, fatty fish and bivalves. Most analytes showed satisfactory accuracy. Alachlor herbicide was found in samples of seabass, mussels, clams and parati with levels ranging between 0.55 to 420.39 μg kg−1 dw. Ethion was found in parati (maximum 211.22 μg kg−1 dw), mussels (15.1 μg kg−1 dw) and clams (maximum 44.50 μg kg−1 dw). Alachlor was found in clams (maximum 93.1 μg kg−1 dw), and bifenthrin was found in parati (maximum 43.4 μg kg−1 dw) and clams (maximum 42.21 μg kg−1 dw). The validated method was satisfactory for the determination of eleven pesticides in the fatty fish matrix, and thirteen pesticides in the samples of lean fish and bivalves. The presence of alachlor, ethion and bifenthrin stands out.