Aquaculture faces the challenge of increasing animal protein production while reducing environmental impact. This study evaluated phosphorus fate and partitioning in monoculture and integrated multitrophic aquaculture (IMTA) systems using a mass-balance approach. The experiment lasted 183 days and was conducted in 12 earthen-bottom ponds (0.015 ha each) comprising four treatments: Nile-tilapia monoculture (TM—Oreochromis niloticus); Nile-tilapia and giant river prawn (TP—Macrobrachium rosenbergii); Nile-tilapia and curimatid (TC—Prochilodus lineatus); Nile-tilapia, giant river prawn, and curimatid (TPC). Phosphorus inputs comprised feed, initial biomass, and water, whereas the outputs included sediment, final biomass, and effluent. Nile-tilapia productivity was significantly higher in the TP system (12,241 kg ha⁻¹) than in the TM monoculture (10,987 kg ha⁻¹). Meanwhile, giant river prawn productivity did not differ between TP (597.05 kg/ha-1) and TPC (569.38 kg/ha-1). Likewise, curimatid productivity did not differ between TC (1,384.66 kg/ha-1) and TPC (1,458.63 kg/ha-1). Feed was the primary phosphorus input, whereas sediment represented the largest phosphorus sink, accumulating more than 2,400 kg ha⁻¹. Water phosphorus was positively correlated with chlorophyll-α (r= 0.49 – 0.74), suspended solids (r= 0.47 – 0.71), and sediment phosphorus (r = 0.52 – 0.65), while being negatively correlated with water transparency (r = -0.55 to -0.72), highlighting the importance of the sediment–water interface in phosphorus dynamics. Phosphorus conversion efficiency and phosphorus use efficiency remained similar among treatments, averaging approximately 17%. Integrated systems altered phosphorus partitioning among compartments, indicating a reorganization of phosphorus flows within the ponds. The inclusion of benthic species, particularly prawns, improved niche complementarity and increased productivity without increasing external nutrient inputs, highlighting the potential of IMTA systems to improve nutrient recycling and sustainability in freshwater aquaculture.