In 2019, the Dutch nitrogen crisis emerged after the Dutch legislation on nitrogen pollution (PAS) was dismissed by the Dutch Raad van State. The crisis resulted in large scale demonstration by farmers and lingering uncertainty in the Dutch business sector. From an ecological perspective the current policy approach is limited as it focusses primarily on reducing the inflow of nitrogen to Natura 2000 areas. Widening the policy approach to better represent the ecological side of the nitrogen crisis provides alternative ecological solution avenues to resolve the crisis. To this end, a System Dynamics model is constructed that encompasses the nutrient cycles of N and P, as well as a level of ecological complexity. To investigate the model’s behaviour under circumstances of deep uncertainty an Exploratory Modelling and Analysis (EMA) approach is used. The results indicate a large potential for cost reduction and increase of ecological performance by aiming policy at ecological compensation instead of emission reduction. The implementation of ecological measures requires scientific substantiation to be accepted into the regulatory framework. The potential economic and societal benefits of an ecological policy approach should be a strong incentive for policy makers and scientists to develop the empirical knowledge for ecological engineering.