An account of the dynamic nature of fish abundance, distribution and stock composition in the Yorkshire Ouse system is presented. In determining in situ energy and nutrient fluxes, knowledge of the magnitude and distribution of fish biomass is important, but the mobility of fishes causes uncertainty in attempts to model the influence of fish biomass on carbon and nutrient fluxes. Data are presented which demonstrate how, within the Ouse system, fish abundance and species composition vary on spatial scales related to physical and biotic environmental parameters, that local abundance may change over short and long time scales and that these changes may be caused by ecosystem perturbations or by response to environmental cues. Opportunities for measuring the influence of spatio–temporal variations on nutrient and energy flux within the Ouse system are discussed.