The Coronel aquifer, located in Chile (36°S – 37°S), has experienced significant water quality deterioration, primarily due to environmental factors and anthropogenic pressures, including increased industrial activities, rising temperatures, and reduced precipitation. These factors synergistically contribute to higher pollutant concentrations. Fluctuations in metal ion levels, particularly total iron and total manganese, have frequently exceeded the regulatory limits for human consumption (0.3 mg L−1 and 0.1 mg L−1, respectively). In response, companies exploiting these aquifers have intensified the search for alternative water sources with better quality. This study analyzed the interannual and seasonal patterns of water quality in the Coronel aquifer, focusing on the hydrogeological sectors of common use (HSCU) in North and South Coronel, alongside hydrogeological measurements and environmental variables. The findings revealed that the North Coronel HSCU is predominantly affected by allochthonous organic pollutants (NO3−), whereas the South Coronel HSCU is impacted by metal pollutants (Fe and Mn). Metal ion concentrations exhibited pronounced interannual and seasonal dynamics, peaking during the summer when precipitation drops below 100 mm month−1 and average monthly temperatures exceed 14 °C. In contrast, NO3− levels did not demonstrate a clear interannual or seasonal pattern. The study suggests that anthropogenic pressures in both HSCU may facilitate the presence of these contaminants.