This study provides comprehensive data on the seasonal variation and distribution of pesticides in the waters bordering Azagny National Park (ANP). Forty-six (46) samples of water from the Azagny area were analyzed using high-performance liquid chromatography (HPLC) coupled with a UV/visible detector to assess the level of thirty-one pesticide molecules divided into six families. These include triazines, phenylureas, organophosphates, carbamates, chloroacetanilides, dicarboximides, and crimidine, which are regularly used in this area. The respective average concentrations of pesticides are 54.54µg//L, 20.93µg/L, 18.24µg/L, 3.06µg/L, and 16.52µg/L in the Bandama, Azagny Canal, ANP, mangroves, and estuarine environment. The analyses also showed that herbicides were the most abundant pesticides in the three waters, Bandama, Azagny Canal, and Azagny Park, with levels of 100%, 63%, and 59%, respectively, followed by insecticides with a levels of 0%, 37%, and 41%, respectively. However, rodenticides (76%) were more frequently detected than herbicides (24% in the mangroves). Regarding seasonal variation, high levels of pesticides were detected in the Bandama River, the Azagny Canal, and the mangroves during the dry season, while multiple pesticide residues were detected during the rainy season. The waters bordering Azagny National Park (ANP) are contaminated with pesticide residues (triazines, phenylureas, organophosphates, carbamates, and chloroacetanilides). As a result, policymakers should implement measures to regularly monitor pesticide levels in plantations surrounding the Azagny region's waters in order to better preserve biodiversity.