Bahia de la Ascension (BA) is a pristine, shallow, karst bay located in the Mexican Caribbean, a region experiencing rapid population growth stimulated by intense tourism development. The overall objective of this study was to address the natural hydrographic variability of this inherently vulnerable ecosystem and assess its influence on a key habitat, the seagrass. The chapters follow the three-branched nature of the study which tackled the connected ecosystem issues of coastal hydrology, physical dynamics of flow and circulation, and the ecological dynamics of the seagrass species Thalassia testudinum in BA. Freshwater input to BA is primarily by submerged groundwater discharges and surface runoff; both sources are derived from fissures in the aquifer but feature distinct water quality due to the interaction with adjacent wetlands. Hurricanes explain 36 percent of the interannual precipitation variability in the region. The water balance indicates a persistent net outflow from BA to the adjacent shelf, suggesting an intense exchange across inlets. Both diurnal and semidiurnal tidal frequencies are attenuated in the inner bay, where a meteorologically-induced subtidal water level increase may occur during four-day southeasterly winds. A clear SW-NE salinity gradient was established during dry and rainy seasons, with a strong tidally-driven marine influence throughout the central basin, and a perennial mesohaline ambient in the southwestern-most bay, where hydrodynamics are primarily controlled by wind stress. Thalassia testudinum is the dominant seagrass species in BA, occupying ~90 percent of the substrate, including the freshwater-influenced inner bay. High nutrient inputs, including phosphorus which might have limiting effects in karst environments, along with the wind-driven circulation controlling water residence times are associated with the successful development of T. testudinum (up to 1,461.23 g DW m-2) within the SW bay. Farthest into the central basin, Thalassia consistently exhibited an inverse correlation between abundance and density of shoots. This pattern was enhanced under exceptional precipitation and inputs of denuded organic matter resulting from hurricanes making landfall on this region. The relationship between nutrient distribution and the above/belowground ratio suggested that Thalassia growing in BA favors the development of the aerial component as nutrients availability increases. This study provides a basic understanding of the most important processes molding the patterns of variability exhibited by T. testudinum in Bahia de la Ascension. The salinity gradient and external nutrient supply, along with the hydrodynamic component, define the spatial scale at which the connectivity between the adjacent wetland, the bay, and the shelf may occur.