The hyporheic zone (HZ), located at the interface of surface and groundwater, is a natural bioreactor for attenuation of chemical contaminants. Engineered HZs can be incorporated into stream restoration projects to enhance hyporheic exchange, with flowpaths optimized to promote biological habitat, water quantity, and water quality improvements. Designing HZs for in-stream treatment of stormwater, a significant source of flow and contaminant loads to urban creeks, requires assessment of both the hydrology and biogeochemical capacity for water quality improvement. Here, we applied tracer tests and high resolution mass spectrometry (HRMS) to characterize an engineered hyporheic zone unit process, called a hyporheic design element (HDE), in the Thornton CreekWatershed in Seattle,WA. Dye, NaCl, and bromide were used to hydrologically link downwelling and upwelling zones and estimate the hydraulic retention time (HRT) of hyporheic flowpaths. We then compared water quality improvements across hydrologically-linked surface and hyporheic flowpaths (3e5m length; ~30 min to >3 h) during baseflow and stormflow conditions. We evaluated fate outcomes for 83 identified contaminants during stormflow, including those correlated with an urban runoff mortality syndrome in coho salmon. Non-target HRMS analysis was used to assess holistic water quality improvements and evaluate attenuation mechanisms. The data indicated substantial water quality improvement in hyporheic flowpaths relative to surface flow and improved contaminant removal with longer hyporheic HRT (for ~1900 non-target compounds detected during stormflow, <17% were attenuated >50% via surface flow vs. 59% and 78% via short and long hyporheic residence times, respectively), and strong contributions of hydrophobic sorption towards observed contaminant attenuation.