This study assessed sediment contamination by heavy metals and pesticide active ingredients linked to chemical inputs used in agricultural activities in the lower Ouémé. Pesticide residues from the organochlorine, pyrethroid and organophosphorus families were investigated by gas chromatography, and heavy metals (Cd, Pb, As, Ni, Zn, Fe, Mg, Cr and Hg) by atomic absorption spectrophotometry. The metallic pollution indices, the contamination factor (CF) and the ecological risk index were calculated. The results revealed 8 active ingredients in the rainy season and 9 in the dry season. Glyphosate was the active ingredient with the highest concentration at all stations, 9.65 ± 0.84 mg/kg recorded in the dry season at the Aguigadji station. All glyphosate values were above the EQS. DDT, Atrazine and Endosulfan also showed high concentrations in the dry and rainy seasons. Emamectin, Abamectin and Lambda Cyhalothrin also showed high concentrations in the dry season at Aguigadji, Ahlan and Sele. Only glyphosate was recorded at the control station (Toho), but in very low concentrations. Lead showed the highest concentrations at all the stations, 265.96 ± 21.02 mg/Kg in the rainy season and 255.38 ± 79.09 mg/Kg in the dry season, all detected at the Aguigadji station and above the EQS. Zn, Ni, Fe, Cu and Cr were all representative in both the dry and rainy seasons at the contaminated stations. Manganese showed high concentrations in the rainy season. Pb showed very high contamination