Nitrogen is essential for seagrass productivity but excesses in nitrogen exposure contribute to declines in meadow health. This study reports baseline data of bulk nitrogen loadings and contents in surficial sediments and seagrass tissues to determine the extent of nitrogen inputs in meadows of Sungai Pulai estuary (Johor, Malaysia). The sediment contained relatively low nitrogen loadings (mean range of 91-94 g N m-2) with likely origins from land-based sources. At the meadow-level, Enhalus acoroides, Cymodocea serrulata and Thalassia hemprichii are the most important species as nitrogen sinks. The highest δ15N values of seagrass tissues were recorded for T. hemprichii (10.7 ± 0.4‰), which indicated an elevated capacity for internal recycling of nitrogen. The data demonstrates the provision of ecosystem services by the meadows in mitigating excess nitrogen imported into the estuary. Seagrasses health, however, needs to be at optimum levels for the effectiveness of the meadow as a nutrient sink.