Aquatic environments experience continuous increases in the concentration of emerging contaminants (ECs) that drive escalating risks toward human health and ecological systems. Studies of material movement patterns across extensive distances will help create effective programs that decrease their propagation. Water bodies are protected against contaminants through physicochemical transformation operations, biological mechanisms, adsorption processes, and degradation and accumulation activities. These processes manage wastes from wastewater discharges, agricultural runoff, and airborne pollutants. Factors like hydrodynamics, sediment interactions, and microbial activity influence the persistence and distribution of these contaminants. Environmental contaminant behavior strongly depends on temperature-controlled parameters, which modify their natural modifications according to recent research findings. Scientists applied high-resolution mass spectrometry and spectroscopic methods to develop detection systems for analyzing transformation processes. Emphasizing computer models’ essential role in predicting pollutant movements throughout the water basins while defining extended operation damage models. Successful resolution of water pollution requires scientists to integrate various research fields. This integration will enable the development of monitoring systems and risk evaluation tools, supported by next-generation water cleanup methods, to protect aquatic environments and human health.