We assessed the uptake of inorganic and organic nitrogen compounds by several macrophytes, epiphytes and phytoplankton in a seagrass meadow. Using double labeled (13C and 15N) substrates of differential complexity, the net transfers from the dissolved nitrogen and carbon pools to phytoplankton, heterotrophic bacteria, seagrasses, and a macroalga were quantified. The phytoplankton compartment was the largest nitrogen sink, but seagrasses dominated carbon fixation. There was a general preference for ammonium over nitrate and urea. Specific uptake rates of individual amino acids were inversely proportional to the complexity of their chemical structure. The bacterial contribution to carbon and nitrogen uptake from amino acids increased for more complex amino acids, as indicated by biomarker-specific measurements (polar lipid-derived fatty acids and D-alanine). Algae-derived dissolved organic nitrogen was taken up by all primary producers, but algae-derived dissolved organic carbon was almost exclusively used by the planktonic compartment. By contrast, a similar composed pool of bacteria-derived dissolved organic matter was not utilized in significant quantities by any of the primary producers. DON should be considered in studies of nutrient dynamics in seagrass meadows, and the role of the planktonic microbial community in seagrass meadows should be investigated in more detail.