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This paper focuses on the comparative analysis and evaluation of the impact of multifunctionality on the agricultural sector for different scenarios that take into account the protection of the environment and natural resources as well as the international trade agreements in the context of the EU agricultural sector. The research focuses on two different regions in Spain that represent the continental agriculture of the region of Castilla-Leon in the northern central plateau and the Mediterranean fertile agriculture of Andalusia in the south. The analysis has been carried out based on mathematical programming models that simulate farmers’ behaviour and their response to the different policy scenarios that correspond to the EU agricultural policies (CAP programmes) and water policies (Water Framework Directive) currently in place. Specifically, these scenarios are: full and partial decoupling, subsidy modulation, crop prices reduction, cross-compliance measures and water pricing policies. Results indicate that the new decoupled CAP will not lead to drastic changes in land use in the two regions studied but will have negative repercussions on farmers’ income. Moreover, the introduction of additional measures, such as cross-compliance, will contribute substantially to improving and protecting the environment even though they amount to an additional cost for farmers. Reduction in crop prices will have significant effects on international trade and is likely to produce a reduction in farm intensification and hence a beneficial effect on the environment but will involve negative socio-economic impacts in marginal rain-fed farms. As regards the integration of agricultural and water conservation policies, the application of the EU Water Framework Directive in conjunction with the new CAP reform would produce different region-specific effects and might question the viability of a number of irrigated farms in Spain.