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Diffuse nitrate leaching from agricultural areas is a major environmental problem in many parts of the world. Understanding where in a catchment nitrate is removed is key for designing effective land use management strategies that protect water quality, while minimizing the impact on economic development. In this study we assess the effects of spatially targeted nitrate leaching regulation in a basin with limited knowledge of the complexity of chemical heterogeneity. Three alternative nitrate reactivity spatial parameterizations were incorporated in a catchment-scale flow and transport model and used to evaluate the effectiveness of four possible spatially targeted regulation options. Our findings confirm that denitrification parameterization cannot be numerically determined based on model inversion alone. Detailed field based characterization using physical and geochemical methods should be considered and incorporated in the numerical inversion scheme. We also demonstrate that there are potential benefits of implementing spatially targeted regulation compared to spatially uniform regulation. Focusing regulation in areas where nitrate residence time is short, such as riparian zones or areas with low natural N-reduction, results in greater reduction of N-discharges through groundwater. Significantly improved efficiencies can be expected when delineation of management zones considers the chemical heterogeneity and groundwater flow paths. These improved efficiencies are achieved by adopting management rules that regulate land use in discharge sensitive areas, where leaching changes contribute the most to the catchment nitrate discharges. In our case study, regulation in discharge sensitive zones was twice as efficient compared to other management options., (Copyright © 2019 Elsevier Ltd. All rights reserved.)