This study aimed to quantify inputs, outputs and accumulation of carbon in integrated multi-trophic aquaculture (IMTA) and monoculture systems of phase II sunshine bass (Morone saxatilis ♂ x Morone chrysops ♀) and giant river prawns (Macrobranchium rosebergii) farmed in stagnant earthen ponds. The experimental design was randomized with three replications of four treatments. The factor tested was the type of production system with four levels: Fish monoculture (FM) with 2 ind/m², Prawn monoculture (PM) with 1 ind/m², Fish-prawn IMTA (IMTA-FREE) with the fish and prawns free-swimming at 2 ind/m² and 1 ind/m², respectively, and fish-prawn polyculture (POLY-CAGE) with the bass reared in cages at 390 ind/cage and the prawns free-swimming at 1 ind/m². Samples of inputs of stocked animals, inlet water, rain, feed, and atmospheric gas and the outputs of harvested animals, total suspended solids, accumulated sludge, settleable solids, harvest water, and gas emissions were collected and analyzed to calculate the carbon budget. Carbon from some samples still being analyzed. Among the more interesting results are that several samples of gas ebullition showed no capture of gas bubbles. Fiberglass funnels floated at the pond surface for 24 hours every two weeks to capture gas bubbles. Presence of gas bubbles indicates that organic carbon is being metabolized anaerobically with nitrate as the principal terminal electron acceptor. The absence of bubbles and the adequate dissolved oxygen (Table 1) indicate that most of the organic carbon was metabolized aerobically.