The purpose of this paper is to investigate the potential gains from changing the existing regulatory framework for fresh water aquaculture production in Denmark. The regulatory framework is changed from an input regulation based on farm-specific feed quotas, to an individual transferable quota system on nitrogen pollution. The regulatory change is analyzed using Data Envelopment Analysis to model the underlying production structure. The effect of allowing trading of nitrogen quotas on production and profitability is analyzed in a joint production model with good and bad output under different behavioral and technical assumptions, whilst keeping the overall pollution level of nitrogen constant. Furthermore, the effect of a catchment area restriction on nitrogen is analyzed to comply with the EU Water Framework Directive. The paper quantifies the gains of a policy change from a command and control system to an incentive based system. The estimated results suggest that the changed regulation could increase Danish aquaculture production by 16 to 55%, whilst actual profitability could be increased 5 to 10 times.