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Inputs, outputs, and accumulation of phosphorus were evaluated for monoculture and polyculture grow‐outs of the Amazon river prawn, Macrobrachium amazonicum and tambaqui, Colossoma macropomum in stagnant earthen ponds using a hypereutrophic water source. A completely randomized experiment was designed with four treatments and three replications: prawn monoculture—monoculture with 30 prawns/m2, fish monoculture—monoculture with 3 fish/m2, integrated multitrophic aquaculture (IMTA)—polyculture with 30 prawns/m2 and 3 fish/m2 reared free swimming, and POLY‐CAGE—polyculture with 30 prawns/m2 and 40 fish/m3 reared in net cages. Samples of commercial diet, water, rain, animals, accumulated sludge, total suspended solids, and settleable solids were collected throughout the experiment to determine the total phosphorus contents of the inputs and outputs and to calculate the phosphorus budget. Results showed high variability in the phosphorus content of each variable in all treatments. Much of the phosphorus was accumulated as solid material at the bottom of the pond (ca. 31–73%). The integrated grow‐outs showed the best phosphorus conversion from the commercial diet (ca. 24–34%) and phosphorus use efficiency from all inputs (ca. 12–18%). Bioturbation from both species appeared to influence the liberation of phosphorus to the water column, stimulating plankton productivity and promoting the turnover of nutrients. A mud‐feeder species should be added to the IMTA systems to take advantage of the large amounts of nutrients in the bottom sediments and increase the uptake of phosphorus by the farmed species. [ABSTRACT FROM AUTHOR]