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A participatory on‐farm study analysed water and nutrient budgets of six low and four high water‐exchange ponds of integrated agriculture–aquaculture (IAA) farms in the Mekong delta. Water, nitrogen (N), organic carbon (OC) and phosphorus (P) flows through the ponds were monitored, and data on fish production and nutrient accumulation in sediments were collected during a fish culture cycle. Results showed that, on average, only 5–6% of total N, OC or P inputs introduced into ponds were recovered in the harvested fish. About 29% N, 81% OC and 51% P accumulated in the sediments. The remaining fractions were lost through pond water discharges into adjacent canals. Fish yields and nutrient accumulation rates in the sediments increased with increasing food inputs applied to the pond at the cost of increased nutrient discharges. High water‐exchange ponds received two to three times more on‐farm nutrients (N, OC and P) while requiring nine times more water and discharging 10–14 times more nutrients than the low water‐exchange ponds. Water and nutrient flows between the pond and the other IAA‐farm components need to be considered when optimizing productivity and profitability from IAA systems.