The implementation of most recent CAP and water policy reforms calls for simulation analytical tools able to quantify socio-economic and environmental impacts that can be different in terms of regions and farm type. This work proposes a territorial mathematical programming model that integrates hundreds of farm models clustered in a single meta-model at regional level that can be easily standardized having the FADN as the main data source. The tool has been experimentally applied to Apulia region and several simulations have been conducted in scenarios differing in terms of agricultural policies (total decoupling, increase of the modulation rate and introduction of a flat rate system for the Single Farm Payment), price of the water resource, market conditions (price of products and cost of inputs). For each simulation, farmers’ choices - cropping patterns and techniques-, the economic assessment of the effects of such choices -revenue, costs and incomes- and environment impacts -use of factors and resulting pressures on natural resources- have been analysed. The results of the analysis show that agricultural policies measures do not affect land use pattern or the agricultural pressure on water resources. But can have major income redistributive effects. On the contrary, water policy and market conditions impact on farmers’ choices, economic performance and environmental pressure.