Seagrass species diversity and abundance were studied in East African back-reef lagoons with contrasting groundwater-outflow rates. The selection of the lagoons was based on a groundwater flow model. A total of 10 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 Thalassia hemprichii showed higher coverage at sites with low groundwater outflow. Porewater salinities were up to 5 psu lower at locations with predicted high groundwater-outflow rates indicating supply of freshwater. The reduction in porewater salinity at groundwater outflow sites is relatively low, which makes it unlikely that a difference in optimum salinity for growth is the main factor causing reduced diversity at these sites. 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 in part, groundwater. Differences in competition for nitrogen may explain the observed pattern in species diversity and abundance. To establish a substantive link between the observed reduced seagrass diversity or enhanced δ 15 N values of T. ciliatum leaves on the one hand and increased groundwater outflow rates on the other, further exploration through detailed measurements of groundwater outflow rates and groundwater nitrogen isotopic composition are needed.