<p>Tropical river–floodplain systems are increasingly threatened by land-use change, hydrological alterations, and climate variability, yet integrated assessments of their ecological condition remain scarce. This study evaluates seasonal and spatial patterns in water quality and trophic status in the lower Usumacinta River basin (southeastern Mexico) and examines the influence of hydrological variability and floodplain wetlands within the Centla Wetlands Biosphere Reserve. Surface water was analyzed at eight stations, both inside and outside the reserve, during a high-discharge rainy season (2017) and a low-discharge dry season (2018), using two complementary multimetric indices: the Water Quality Index (WQI) and the Trophic Index (TRIX). Hydrological state was the primary organizing gradient. During the rainy season, elevated discharge increased suspended solids and total nutrient loads, lowered dissolved oxygen, and heightened eutrophication signals, particularly in floodplain and estuarine reaches. In contrast, the dry season showed improved overall water quality but higher dissolved inorganic nitrogen and stronger phosphorus limitation. Spatially, the San Pedro River maintained oligotrophic conditions and high ecological integrity, whereas the Grijalva River remained persistently eutrophic, reflecting cumulative anthropogenic pressures. Although floodplain wetlands were associated with localized nutrient attenuation under certain hydrological conditions, their regulatory influence was context-dependent and constrained by discharge and land-use gradients. By integrating hydrological context with multimetric indices, this study demonstrates that seasonal connectivity, rather than simple dilution, governs water quality responses in large tropical rivers. These findings provide a basin-scale framework for anticipating eutrophication risk under intensifying hydroclimatic and anthropogenic pressures.</p>