In coastal lagoons, marine benthic macrophyte meadows can be an important element in the resistance to eutrophication of the ecosystem, as they can function as temporary nitrogen sinks, limiting the availability of this nutrient for opportunistic organisms. The role of nitrogen sinks for two dominant macrophyte species of Mediterranean coastal lagoons, the seagrass Cymodocea nodosa and the seaweed Caulerpa prolifera, was analysed by two different approaches: (i) studying nitrate (NO3-) and ammonium (NH4+) uptake kinetics of aboveground tissues in a laboratory and (ii) estimating nitrogen stocks and demands of meadows under natural conditions. The studies were carried out in the coastal lagoon of the Mar Menor, which has been subjected to high anthropogenic nitrogen inputs for decades. While both macrophytes were efficient in exploiting NH4+ from the water column, only C. prolifera showed a high NO3- uptake capacity. Large N pools in the C. nodosa and C. prolifera meadows of the Mar Menor were detected, suggesting that these habitats may have the potential to be essential reservoirs for this nutrient. However, the major role of belowground tissues of the seagrasses in nitrogen accumulation may determine important differences between the two species in temporary N storage and sequestration. The data on N demands for the meadows of both macrophytes in the Mar Menor suggest an important contribution of these habitats in controlling the inputs of this nutrient into the lagoon. We conclude that C. nodosa and C. prolifera meadows can play a key role as a sink for dissolved inorganic nitrogen in temperate coastal lagoons, being an important mechanism of resistance to eutrophication.