This mini-review delves into the intricate interplay between agricultural practices and aquatic environments, highlighting the global imperative to enhance water quality. Drawing insights from diverse sources, it underscores the complex web linking water management and agriculture with the health of aquatic ecosystems. The expansion and intensification of agriculture have led to widespread fertilizer and pesticide use, impacting the water quality of groundwater, rivers, lakes, and marine habitats. Large-scale irrigation systems, while vital for food security, have inadvertently contributed to land and water salinity issues. As agricultural activities intensify, they often alter aquatic ecosystems, affecting aquatic fauna and overall ecosystem functioning. The sustainable use of chemicals and organic farming practices is paramount in mitigating environmental and ecological impacts. In the context of global changes, the adoption of ecologically based agricultural management strategies holds promise for enhancing sustainability and reducing off-site consequences. The mini-review emphasizes that integrated water resource management, advanced agricultural practices, and rigorous regulation are essential for tackling critical water quality and quantity challenges linked to agriculture.