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A total of ten seagrass species was observed at all sites together. Sites with a higher groundwater outflow displayed a lower species diversity than sites with a lower groundwater outflow. Thalassodendron ciliatum dominated at sites with high groundwater outflow rates, while Thalssia hemprichii showed higher coverage at sites with low groundwater outflow. Porewater salinities were significantly lower at locations with high groundwater-outflow rates indicating supply of freshwater. Nitrogen stable isotope signatures of seagrass leaves showed a significant increase with increased groundwater-outflow rates. This suggests that the nitrogen source for these plants was, at least for a part, groundwater. In addition, lagoons with high densities of the human population had highest 15N values, indicative of anthropogenic nitrogen inputs. Differences in optimum salinity for growth between species and competition for nitrogen may explain the observed pattern in species diversity and abundance.