The Nitrates Directive (91/676/EEC) offers EU Member States the unique choice to apply the nitrate regime in either designated areas or on their entire territory. The Netherlands has opted for a whole territory approach but is tempted to change this policy. This article investigates the legal options of the Netherlands to switch from a whole territory approach to a designated area approach. It also investigates two alternative possibilities to create a more area-based implementation of the Nitrates Directive in the Netherlands within a whole territory approach. The alternatives are (i) a further differentiation of the current manure policy and (ii) the possibility to integrate the implementation of the Nitrates Directive and the Water Framework Directive. The results of the research are placed in a European perspective.