Water quality assessment is a key factor in the environmental management of freshwater networks, especially those including fish farms, which need cost-effective operational tools to monitor and control their waste output. In France, current legislation specifies limits 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 the environmental impact of trout farms on aquatic ecosystems and to compare waste assessment methods, we monitored 20 commercial flow-through trout farms for 24 h, and we compared data obtained with the two methods (hydrological method and mass balance modelling) by linear regression. For total nitrogen and total phosphorus, the correlation between the two methods was high; thus, considering the uncertainty of both methods, this study was not able to determine which was more accurate. The high correlation between observed ammonia concentrations and predicted total nitrogen emissions provides a coefficient for estimating ammonia emissions at the farm level. The same approach is proposed for the evaluation of phosphate emissions. In conclusion, this study confirms the utility of simulation modelling for assessing nutrient release from fish farms.