Nitrate pollution from agriculture is an important environmental externality, caused by the excessive use of fertilizers. The internalization of this problem, via a tax on mineral nitrogen, could lead to a second best solution, reducing nitrate emissions. Several authors suggest that a reduction in agricultural support could produce similar results. In this paper, we examine the effects of different levels of a uniformly implemented nitrogen tax in France under two policy scenarios, corresponding to post Agenda 2000 and 2003 Luxembourg reforms of European Union's Common Agricultural Policy, in order to reveal the synergies and conflicts between the tax and the policy scenarios in terms of nitrate emissions abatement. The analysis is performed at different geographical scales, from the national to the regional and is based on a bioeconomic approach that involves the coupling of the economic model AROPAj with the crop model STICS. Results show that the efficiency of the N-tax varies according to the geographical scale of the analysis and the type of farming. Furthermore, we prove that a uniform implementation may lead to perverse effects that should always be taken into account when introducing second-best instruments. © 2012 Springer Science+Business Media B.V.