Water quality decline is evident in areas of farming intensification in the Southland region of New Zealand. However, regardless of similar landuse pressures, there is significant spatial variation in water quality outcomes. To optimise water management expenditure, the accumulation and transport of farm contaminants through soil, groundwater, and into streams and rivers must be understood. This work utilises a systems integration approach to explain the spatial variability in the hydrochemical and water quality signatures of freshwaters. Precipitation (rain, hail and snow), soil, soil water, ground‐ and surface water samples were analysed and cross‐referenced against existing spatial frameworks of topography, geomorphology, hydrology, hydrogeology and soils. This included classifying waters with common origins and identification of the controls or ‘drivers’ over water composition. Four key drivers of surface water and shallow groundwater composition were identified and mapped for the Southland region: (i) precipitation source; (ii) water source and recharge mechanism; (iii) combined soil and geological reduction potential, and; (iv) geomorphic surface age and substrate (rock and sediment) composition. Maps for each driver layer spatially depict driver gradients across the region that influence different aspects of water composition and quality. Each driver layer is a distillation of (multiple) critical characteristics of pre-existing spatial frameworks (e.g. soils maps, Q-Map, REC, DEM, hydrogeology). We demonstrate that: (i) through combination of each of the key spatial drivers it is possible to estimate the steady-state water composition of regional surface waters and shallow unconfined groundwaters with a high degree of confidence, and; (ii) that unique assemblages of driver layers can be used as a basis for targeted land use management to improve water quality.