Intense farming is often associated with the excessive use of manure or fertilizers and the subsequent deterioration of the groundwater quality in many aquifers worldwide. Stable isotopes of dissolved nitrate (δ N and δ O) are widely used to determine sources of nitrate contamination and denitrification processes in groundwater but are often difficult to interpret. Thus, Monte Carlo simulations were carried out for a site in lower Bavaria, Germany, in order to explain δ N observations in a porous groundwater system with two aquifers, the main aquifer (MA) and several smaller perched aquifers (PA). For evaluating potential contributions, frequency distributions of δ N were simulated deriving from (I) the mixing of different nitrate sources, related to land use, as input to groundwater, combined with (II) transport of nitrate in groundwater and (III) microbial denitrification. Simulation results indicate a source-driven isotopic shift to heavier δ N values of nitrate in groundwater, which may be explained by land use changes towards a more intensified agriculture releasing high amounts of manure. Microbial denitrification may play a role in the PA, with simulated δ N distributions close to the observations. Denitrification processes are however unlikely for the MA, as reasonable simulation curve fits for such a scenario were obtained predominantly for unrealistic portions of nitrate sources and related land use. The applied approach can be used to qualitatively and quantitatively evaluate the influence of different potential contributions, which might mask each other due to overlapping δ N ranges, and it can support the estimation of nitrate input related to land use. This article is protected by copyright. All rights reserved.