The aim of the study is to investigate the variability in riverbed permeability fields in an unprecedented spatial resolution and quantify the impacts on controlling hyporheic exchange fluxes. Geophysical surveys were conducted deploying GPR on the floodplain and within the channel. At locations identified to be representative for the range of streambed hydrofacies in investigated stream reach, multi-level mini-piezometer networks were installed in the streambed. The results of GPR surveys in both sites provided different radar reflections which indicated a range of different radar facies and helped to delineate the type and extend of high and low conductive materials. The localised high Darcy fluxes inside high conductivity piezometers indicated rapid discharge of groundwater due to the enhanced connectivity to deeper groundwater. Whereas, low flow velocity within and around low conductivity peat and clay lenses indicated that these layers substantially inhibit groundwater upwelling, resulting in enhanced streambed residence and reaction times. The increase in residence time and the related depletion in the volume of DO facilitated the development of conditions necessary for nitrate reduction. In contrast, preferential flow paths and short residence times in highly conductive drift deposits resulted in no significant changes in nitrate concentrations along hyporheic flow paths.