The assessment of the status and trend, in concentrations and loads, required for regulations such as the European Water Framework Directive, through monitoring, is complex due to spatial and temporal variability in driving forces (natural as well as man induced), biogeochemical processes in surface and ground water, groundwater-surface water interaction processes and transport processes. In the past years, innovative devices and sensors have been developed, with which high resolution monitoring as well as time averaged sampling become feasible. The new development yields enormous data sets, enabling the identifications of water and nutrient pathways, improving our knowledge on biogeochemical processes and the quantification of groundwater-surface water interactions. In this special issue we welcome papers dealing with new high resolution as well as time-integrated monitoring strategies of flow and nutrient concentrations, that can be transformed into more reliable loads estimates, including the transformation from data into information to support management policies. Amongst others the objectives of the monitoring might be: process understanding; identification of pathways; effectiveness of mitigation measures, or support of modelling. Technical issues may include spatial monitoring design; scaling and different spatial resolutions; assessment of pathways; groundwater-surface water interactions; and the cost-effectiveness of monitoring strategies.