AbstractA data set describing annual variation of water quality in ten commercial channel catfishIctalurus punctatusponds was subjected to exploratory statistical analysis to infer ecological processes affecting pond water quality. Two factors explained 67% of the variation in concentrations of water quality variables. The first factor (Factor 1) explained 49% of the variance and was associated with a large negative loading by total ammonia‐nitrogen and large positive loadings by total nitrogen, total phosphorus, chemical oxygen demand, and chlorophylla. Factor 1 was interpreted with respect to factor loadings to represent the effect of phytoplankton biomass. The second factor (Factor 2) explained an additional 18% of the variance and was associated with a large negative loading by soluble reactive phosphorus and large positive loadings by nitrite‐nitrogen and, to a lesser extent, nitrate‐nitrogen. Factor 2 was interpreted to be related to variation in pond sediment oxygenation. Although factor analysis indicated the overwhelming effect of phytoplankton biomass on water quality, opportunities for management of phytoplankton communities in large commercial aqua‐culture ponds are limited. However, maintenance of an oxidized sediment‐water interface may improve water quality by limiting the diffusion of reductant‐soluble phosphorus from sediment to water and increasing sediment nitrific