There is increasing interest in intensive production of Ictalurid catfish in the United States and a better understanding of water quality dynamics in intensive culture is needed. Budgets for water, nitrogen, and phosphorus were estimated over a production season (March–November) for an In-pond Raceway System for channel catfish, Ictalurus punctatus, and hybrid catfish, I. punctatus×I. furcatus, with co-culture of paddlefish, Polyodon spathula, and Nile tilapia, Oreochromis niloticus. In addition to the rainfall and runoff, 70 cm of water was applied from a well to offset evaporation and seepage. Production of each kilogram of live catfish required 1.50 kg of feed and released 51.7 g nitrogen and 9.7 g phosphorus. Harvest of catfish accounted for 34.0% of nitrogen and 37.1% of phosphorus applied in feed. Seepage and overflow removed only small portions of nitrogen and phosphorus, while denitrification and ammonia volatilization removed large amounts of nitrogen. Some nitrogen accumulated in sediment. Phosphorus was harvested in fish and absorbed by pond sediment. Mechanical aeration aided in maintaining appropriate dissolved oxygen levels for fish production.