This dataset contains the input data, intermediate calculations, and final results used to construct comprehensive nutrient budgets (C, N, and P) in experimental fishponds with different species compositions, including Nile tilapia, grass carp, and polyculture systems. It includes measurements of water, sediment, and fish biomass, feed inputs, and derived fluxes such as sedimentation, water inflow/outflow, and unaccounted losses. Calculations incorporate carbon and nitrogen concentrations, C:N ratios, and mass balances across compartments, allowing detailed assessment of nutrient cycling and efficiency in aquaculture systems.