Summary Tropical marine seagrasses live in environments with low nutrient concentrations. However, as land development intensifies along tropical coastlines, the marine environment in which these organisms grow is becoming more nutrient‐rich. Nitrogen (N) uptake, assimilation, translocation and storage under a diversity of N sources in enriched conditions were investigated in two tropical seagrass species, Cymodocea serrulata and Thalassia hemprichii, from an oligotrophic marine environment. Both seagrasses were able to take up different inorganic and organic N sources through their above‐ and belowground tissues when enriched with high N concentrations. The uptake rates of T. hemprichii were generally higher than C. serrulata in leaves and rhizome, whereas root uptake was systematically higher in C. serrulata. Acropetal and basipetal translocation was observed in both species. Reduction and assimilation of N, measured in terms of their nitrate reductase and glutamine synthetase activity, were correlated with nitrate and ammonium uptake rates, respectively. Cymodocea serrulata showed a tendency to immediately use the available N, whereas T. hemprichii allocated more N in assimilation and storage investment. The responses of these seagrasses to N‐enrichment demonstrate their ability to adapt to over‐enrichment by varying N sources in the first step of the eutrophication process.