Lagoon systems are characterized by high dynamic variability influenced by seasonal cycles, such as dry periods, northern cold fronts, and tropical monsoons. This study aims to characterize the hydrogeology of the Chaschoc-Sejá lagoon system (located in Tabasco, Mexico), to provide a scientific basis for sustainable water management. Understanding these fluctuations is a key role for maintaining ecological balance and supporting local communities reliant on these water bodies. The research employed an integrated approach combining hydrometry, meteorological data, and remote sensing tools. Specifically, the study used Sentinel satellite imagery to monitor land cover and flood extents, alongside data from the Surface Water and Ocean Topography (SWOT) mission to achieve high-resolution measurements of water surface elevations and storage changes. These products allowed for a spatiotemporal analysis of the system's hydrological behavior. The findings show a congruent and repetitive annual pattern between seasonal cycles and flood surface areas. Despite the system's recharge capacity, the water balance analysis indicates a negative balance during 7 out of 12 months of the hydrological year. This suggests a significant period of water deficit that drives the system’s seasonal contraction. The integration of SWOT and Sentinel products proved a fundamental integration for evaluating both the immediate seasonal dynamics and the long-term water functioning of the Chaschoc-Sejá system. These results underscore the vulnerability of the lagoon to prolonged dry seasons and provide a vital framework for developing adaptive management strategies to ensure the system's long-term hydrological sustainability.