Aquatic habitats are seriously threatened by agricultural runoff, which has a negative impact on fish health. Water bodies are exposed to agrochemicals from fertilizers, pesticides, and herbicides, which alter their physiology, genetic makeup, and behavior. These pollutants create neurological problems that upset aquatic food webs, impede reproductive, genotoxicity, bioaccumulation, weakened immunity, and increased risk of disease. Monitoring is improved by the early detection of stress reactions made possible by advances in omics technologies like proteomics and metabolomics. In addition to ecological consequences, runoff causes economic harm, fisheries losses, and hazards to human health by contaminating food systems. For mitigation to guarantee ecosystem resilience, buffer zones, less chemical use, and wetland restoration are necessary.