Abstract. The hyporheic zone is a hotspot of biogeochemical turnover and nutrient removal in running waters. However, nutrient fluxes through the hyporheic zone are highly variable in time and locally heterogeneous. Resulting from the lack of adequate methodologies to obtain representative long-term measurements, our quantitative knowledge on transport and turnover in this important transition zone is still limited.In groundwater systems passive flux meters, devices which simultaneously detect horizontal water and solute flow through a screen well in the subsurface, are valuable tools for measuring fluxes of target solutes and water through those ecosystems. Their functioning is based on accumulation of target substances on a sorbent and concurrent displacement of a resident tracer which is previously loaded on the sorbent.Here we evaluate the applicability of this methodology for investigating water and nutrient fluxes in hyporheic zones. Based on laboratory experiments we developed hyporheic passive flux meters (HPFMs) with a length of 50 cm which were separated in 5–7 segments allowing for vertical resolution of horizontal nutrient and water transport. The HPFMs were tested in a 7 day field campaign including simultaneous measurements of oxygen and temperature profiles and manual sampling of pore water. The results highlighted the advantages of the novel method: with HPFMs, cumulative values for the average N and P flux during the complete deployment time could be captured. Thereby the two major deficits of existing methods are overcome: first, flux rates are measured within one device instead of being calculated from separate measurements of water flow and pore-water concentrations; second, time-integrated measurements are insensitive to short-term fluctuations and therefore deliver more representable values for overall hyporheic nutrient fluxes at the sampling site than snapshots from grab sampling. A remaining limitation to the HPFM is the potential susceptibility to biofilm growth on the resin, an issue which was not considered in previous passive flux meter applications. Potential techniques to inhibit biofouling are discussed based on the results of the presented work. Finally, we exemplarily demonstrate how HPFM measurements can be used to explore hyporheic nutrient dynamics, specifically nitrate uptake rates, based on the measurements from our field test. Being low in costs and labour effective, many flux meters can be installed in order to capture larger areas of river beds. This novel technique has therefore the potential to deliver quantitative data which are required to answer unsolved questions about transport and turnover of nutrients in hyporheic zones.