This study investigates metallothionein gene expression in Biomphalaria alexandrina as a biomarker for pesticide stress and examines bacterial abundance in pesticide-contaminated water in Gharbeya, Egypt. Pyrethroids and triazoles were detected in water and sediment samples, exceeding WHO limits. Cypermethrin, deltamethrin, and epoxiconazole accumulated in B. alexandrina snails in winter, while tetraconazole accumulated in spring and autumn. The bioconcentration factor (BCF) for deltamethrin was highest in snails in winter, corresponding with greater deltamethrin residues in water during that season compared to summer. Snails showed the highest Metallothionein (MT) levels in summer (5.79 ± 0.01), even with greater pesticide bioaccumulation in winter, suggesting that MT may help manage pesticide toxicity. Bacterial strains from sediment samples (8 spcies) were more numerous than those from water samples (4 species), suggesting that sediments enhance nutrient availability and provide stable habitats. Correlations between bacterial species and pyrethroid and triazole residues suggest their potential in future bioremediation studies. These findings support SDG 14 and SDG 6 by safeguarding aquatic biodiversity and water quality in contaminated ecosystems. © The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2026.