Water regulation and purification (WR) function is defined as “the capacity of the soil to remove harmful compounds and the capacity of the soil to receive, store and conduct water for subsequent use and to prevent droughts, flooding and erosion.” It is a crucial function that society expects agricultural soils to deliver, contributing to quality water supply for human needs and in particular for ensuring food security. The complexity of processes involved and the intricate tradeoff with other necessary soil functions requires decision support tools for best management of WR function. However, the effects of farm and soil management practices on the delivery of the WR function has not been fully addressed by decision support tools for farmers. This work aimed to develop a decision support model for the management of the WR function performed by agricultural soils. The specific objectives of this paper were (i) to construct a qualitative decision support model to assess the water regulation and purification capacity of agricultural soils at field level, to (ii) conduct sensitivity analysis of the model; and (iii) to validate the model with independent empirical data. The developed decision support model for WR is a hierarchical qualitative model with 5 levels and has 27 basic attributes describing the soil (S), environment (E), and management (M) attributes of the field site to be assessed. The WR model is composed of 3 sub-models concerning (1) soil water storage, (2) P and sediment loss in runoff, and (3) N leaching in percolating water. The WR decision support model was validated using a representative dataset of 94 field sites from across Europe and had an overall accuracy of 75% when compared to the empirically derived values across these sites. This highly accurate, reliable, and useful decision support model for assessing the capacity of agricultural soils to perform the WR function can be used by farmers and advisors help manage and protect their soil resources for the future. This model has also been incorporated into the Soil Navigator decision support tool which provides simultaneous assessment of the WR function and other important soil functions for agriculture.