Food security in Asia depends significantly on small-scale pond aquaculture in which fish feed on external feeds and natural food resources. Little is known about the assimilation of natural food resources into fish. In order to elucidate the food web and nitrogen flows in a traditionally and a semi-intensively managed pond in Vietnam, d 13 C and d 15 N in pond inputs and fish were measured before and after the application of inorganic 15 N at 1.1 and 0.4 % of total nitrogen. The applied 15 N was traced through the biomass of stocked fish over 30 days. Under traditional management, grass carp was the dominant species in number and biomass. After 30 days, grass carp assimilated 1.2 % of the applied tracer through natural food resources. Filter feeders assimilated only 0.1-0.3 % of the tracer after 30 days because of the limited productivity in the traditionally managed pond. Nile tilapia showed the highest uptake rates over the 30 days, which demonstrated their ability to feed on a variety of natural food resources. In total, 2.6 % of the applied 15 N was assimilated into fish biomass after 30 days. Under semi-intensive management, common carp was the main species numerically and assimilated 1.8 % of the tracer after 30 days. Grass carp was stocked at lower density, but had the highest biomass by the time of the experiment. Grass carp assimilated 0.2 % of the applied tracer suggesting a low contribution of natural food resources to its nutrition. Silver carp benefited most from the higher natural food resources. In total, 4.1 % of applied 15 N was assimilated into fish biomass after 30 days. Traditional small-scale aquaculture of a grass carp-dominated polyculture has a lower assimilation efficiency of applied fertilizers into fish biomass than a common carp-dominated polyculture under semi-intensive management.