Strategies of groundwater protection in agricultural dominated areas are mainly based on a general reduction of the input of nutrients like nitrate. However, preventive measures in different parts of the catchment may provide very different effects on raw water quality. Exemplified on the case study 'Liedern' (BEW GmbH Bocholt, Germany) it is shown that hydrogeochemical processes along the flow path and in the well strongly affect the results of agricultural measures in terms of modality and efficiency. Thus, a reduction of fertilization in the vicinity of the well gallery leads to a decrease of nitrate concentration in the raw water. Whereas agricultural measures in the eastern part of the catchment do not influence nitrate, but cause a reduction of the iron concentration and rate of incrustation in the wells after 18 years. In this study we present a management tool that enables assessment of future trends in raw water quality. The tool is based on a reactive transport model which considers land use dynamics as an instrument to influence groundwater/raw water quality. A thermodynamic equilibrium approach is applied for modelling hydrogeochemical processes between aqueous, solid and gaseous phases. Kinetically controlled reactions like the microbial degradation of organic carbon are expressed by multiplicative Michaelis-Menten equations.