A series of boreholes of up to 50 m depth, drilled into Lower Palaeozoic mudstone, shale and greywacke bedrock in the headwater catchment areas of the River Severn at Plynlimon in Central Wales, shows an extensive chemically- and hydrologically-active shallow groundwater fracture flow system. Groundwater chemistry varies in space and time with lowest water levels and highest alkalinities occurring during the drier summer months. The groundwaters are enriched in base cations, silica, sulphate and alkalinity relative to surface waters indicating significant silicate weathering sources and sulphide oxidation. These sources provide important contributions to both stream water quality and flow. At one site, the introduction of a borehole near to the main river opened bedrock fractures which increased the amount of groundwater entering the river. This had a profound effect on the river water quality by increasing the pH, alkalinity and calcium concentrations. As well as pointing to the possibility of the wider availability of groundwater resources in upland areas, the results highlight (a) the potential value of groundwater as a acid neutralizing resource, (b) the importance of weathering processes and flow routing within the groundwater environment for stream water chemistry, (c) the potential for altering stream water quality by manipulation of groundwater routing and (d) the need to include groundwater characteristics in hydrochemical management models of surface water acidification.