Heavy metal pollution in aquatic ecosystems is a critical environmental issue worldwide. In these ecosystems, the seston adsorbs heavy metals from the water and introduces them into the food web, causing potential environmental and health risks. This study analyses how heavy metals (Cd, Hg, Cr, Cu, Pb, Fe, and Mn) are distributed in the water and seston of the Tampamachoco Lagoon, an ecosystem affected by pollution from a thermoelectric plant and by hydrometeorological variability, both of which influence their concentrations. The relationships among metal distribution, physicochemical variables, and the influence of plant emissions in three seasons (rainy, northerly windstorms, and dry) were analyzed. The metal concentrations in seston (Fe > Mn > Pb > Cu > Cr > Hg) were up to four times higher than in the water column (Fe > Mn > Cr > Cd > Pb > Cu > Hg), emphasizing the key role of particulate matter in metal transport and bioavailability. Particularly, the Cd concentrations exceeded WHO thresholds by 527.6% in the water column during the rainy season, while Hg and Pb exceeded the thresholds of the Mexican criteria for the protection of marine aquatic life by 4.05% and 41.6%, respectively. Principal Component Analyses revealed distinct spatiotemporal distribution patterns for metals in water and seston, reflecting the combined effects of natural variability and anthropogenic inputs. The strong association between metals and seston indicates continued contamination and potential risks to aquatic ecosystems. These findings highlight the environmental impact of metals on seston and the need for monitoring to assess aquatic ecosystems’ health. Our results highlight the importance of understanding how metals are distributed between seston and water, and how climate variability affects pollutant redistribution patterns. We propose that water quality regulations need to be rethought and redirected towards the achievement of new strategic objectives that truly integrate the different pollutant sources whose final destination is water bodies, so as to protect and conserve biodiversity and aquatic ecosystems.