Water quality assessment is a key factor in the environmental management of freshwaternetworks, especially those including fish farms, which need cost-effective operationaltools to monitor and control their waste output. In France, current legislation specifieslimits in concentrations of dissolved compounds and suspended solids at fish-farm outlets.Despite the development of mass-balance modelling tools, chemical analysis of water(hydrological method) remains the most widely used method. To understand better theenvironmental impact of trout farms on aquatic ecosystems and to compare waste assessmentmethods, we monitored 20 commercial flow-through trout farms for 24 h, and we compareddata obtained with the two methods (hydrological method and mass balance modelling) bylinear regression. For total nitrogen and total phosphorus, the correlation between thetwo methods was high; thus, considering the uncertainty of both methods, this study wasnot able to determine which was more accurate. The high correlation between observedammonia concentrations and predicted total nitrogen emissions provides a coefficient forestimating ammonia emissions at the farm level. The same approach is proposed for theevaluation of phosphate emissions. In conclusion, this study confirms the utility ofsimulation modelling for assessing nutrient release from fish farms.