The integrated modelling system INITIATOR was applied to a landscape in the northern part of the Netherlands to assess current nitrogen fluxes to air and water and the impact of various agricultural measures on these fluxes, using spatially explicit input data on animal numbers, land use, agricultural management, meteorology and soil. Average model results on NH 3 deposition and N concentrations in surface water appear to be comparable to observations, but the deviation can be large at local scale, despite the use of high resolution data. Evaluated measures include: air scrubbers reducing NH 3 emissions from poultry and pig housing systems, low protein feeding, reduced fertilizer amounts and low-emission stables for cattle. Low protein feeding and restrictive fertilizer application had the largest effect on both N inputs and N losses, resulting in N deposition reductions on Natura 2000 sites of 10% and 12%, respectively.