Nitrogenous compounds such as ammonia, nitrate, and dissolved organic nitrogen (DON) are the main waste components of marine fish pond effluents. These compounds are also regarded as the primary nitrogen sources for seaweed. Aiming at designing an efficient and cost-effective extractive biofilter for fishpond effluents, Ulva lactuca performance and the dynamics of dissolved inorganic (DIN) and DON uptake by this alga grown in the effluents of a land-based integrated multi-trophic aquaculture (IMTA) system were studied. Stocking densities of 1 and 3 kg m−2 were found to be optimal for yield along with specific growth rate (SGR) and protein content, respectively. The presence of ammonia inhibited nitrate uptake by U. lactuca and carbon limitation reduced SGR and yield. However, protein levels of U. lactuca tissue in a carbon-limited situation were higher than when unlimited carbon was made available. When compared with 3 kg m−2 stocking densities, the high C/N ratio in U. lactuca tissue cultured at 1 kg m−2 likely indicated carbon limitation. Ammonia assimilation rate was density dependent. At 1 kg m−2, ammonia uptake was relatively fast, at 4.31 μmole N h−1, and nitrate uptake started only 24 h after ammonia depletion, suggesting this period to be the time required for nitrate reductase (NR) synthesis in the algae tissue. At 2 kg m−2, ammonia uptake was 2.51 μmole N h−1 and nitrate uptake started 24 h after that observed in 1 kg m−2, suggesting that the lower ammonia threshold for uptake by the U. lactuca is around 1.4 μmole L−1. Contrary to 1 and 2 kg m−2 stocking densities, in the 3 kg m−2 stocking density, ammonia uptake was as low as 1.51 μmole N h−1 and no uptake of nitrate appeared to have taken place due to the presence of ammonia in the water. The additional ammonia in the water was found to be due to DON-ammonifying bacteria on the surface of U. lactuca thalli. In the 1ow stocking density, the additional ammonia was relatively low compared to that measured at the high algae density. In the light of the better understanding of the system dynamics achieved in our study, we hypothesize that a set of similar bioreactors using U. lactuca can intensify the system purification efficiency manifold.