Passive sampling is a well-established tool for monitoring time-weighted average concentrations of polar and semi-polar organic contaminants in streams at flow velocities between 0.1 and 0.4 m s⁻¹. However, its application under low-flow conditions (10⁻⁵ to 0.01 m s⁻¹) – as encountered in hyporheic zones – has been scarcely reported. In this study, 3 novel passive sampler configurations were developed for the monitoring of (semi-)polar organic pollutants and related transformation products across the water-sediment interface and thus across varying hydrodynamic conditions. Their design was inspired by Chemcatcher and diffusive gradients in thin films for organics. To determine the most optimal sampler design, an uptake experiment was completed involving the 3 novel passive sampler configurations and a reference Chemcatcher in polar configuration. The experiments consisted of a circular flume that simulated the main channel of a stream and an aquarium with stagnant water that represented the underlying hyporheic zone. The systems were exposed to 192 organic pollutants at environmental concentrations, and the samplers were then collected, extracted and analyzed using liquid chromatography high-resolution mass spectrometry after 2, 6 and 14 days. The configuration that was most insensitive to different hydrodynamic conditions consisted of a reversed-phase sulfonated styrenedivinylbenzene disk as the receiving phase that was covered by an agarose diffusion gel and topped with a polyethersulfone membrane filter. To further evaluate its environmental application, samplers were installed downstream of a sewage treatment plant located at an urban stream in Berlin, Germany (Erpe). The samplers were mounted on custom-made holders which were subsequently embedded in the stream bed to position samplers above (0.30 m) and within the sediment (−0.15/-0.30/-0.45 m) for 11 days. Target and suspect screening workflows were then applied to identify common concentration patterns and link parent attenuation to transformation product formation. A total of 104 concentration profiles were determined, suggesting the efficiency of the proposed sampling strategy in the water-sediment interface. Valsartan acid was the only known transformation product indicative of hyporheic zone-driven attenuation as its concentration in porewater by far exceeded its concentration in surface water. Similar patterns were observed for a larger list of suspected transformation products, of which a sotalol transformation product was tentatively identified. Overall, the established sampling methodology can be effectively used to quantify organic contaminants during low-flow conditions and is suitable for the characterization of attenuation patterns of organic pollutants in hyporheic zones.