Pesticide contamination has become a global concern. Pesticides can sorb onto suspended particles and deposit into the sedimentary layers of aquatic environments, resulting in ecosystem degradation, pollution, and diseases. Pesticides impact the behavior of aquatic environments by contaminating organic matter in water, which serves as the primary food source for aquatic food webs. Pesticide residues can increase ammonium, nitrite, nitrate, and sulfate in aquatic systems; thus, threatening ecological environment and human health. Several physical, chemical, and biological methodologies have been implemented to effectively remove pesticide traces from aquatic environments. The present review highlights the potential consequences of pesticide exposure on fish and humans, focusing on the (epi)genetic alterations affecting growth, behavior, and immune system. Mitigation strategies (e.g., bioremediation) to prevent/minimize the detrimental impacts of pesticides are also discussed. This review aims to shed light on the awareness in reducing the risk of water pollution for safe and sustainable pesticide management.