Effects of organic-waste loading from fish farming on benthic metabolism and nitrogen (N) cycling were studied in the tropical Nha Phu Estuary, Vietnam. The loading of fish excreta and feed waste enhanced benthic oxygen (O2) uptake two times and total carbon dioxide (TCO2) release three times, compared with the reference station. NH4+ was the major form of released N, comprising 94–100% of dissolved inorganic N (DIN) flux below and near fish cages. Only 3% and 1% of organic carbon (OC) and organic N (ON) deposited from the fish farm was degraded in the sediment, whereas the rest was dispersed to adjacent areas via tidal currents or buried into the sediment. Coupled nitrification–denitrification were almost 0 under fish cages but increased at distances greater than 10 m from fish cages. Consequently, biologically available N was not removed permanently near fish cages as the excess N deposited under cages were mineralised and released as DIN. The nutrient efflux could therefore potentially be a source for pelagic primary production in the vicinity of cages. However, the water currents and low water residence time may have distributed and diluted the nutrient effect of cages to the entire estuary and the adjacent ocean.