Transformation and retention of nitrogen and other biologically reactive solutes in the hyporheic zones of running water contribute to an essential ecosystem service. However, the synoptic impact of intense agricultural or urban land-uses, elevated nutrient loading, flow alterations, riparian clear-cutting, and channelization on the source-sink behavior of solutes in hyporheic zones remains largely uncharacterized and unquantified. Therefore, we studied nutrient dynamics in a hydromorphologically and chemically modified stream reach using a new monitoring approach allowing the simultaneous measurement of nutrient and water flux through a screened area in the subsurface of rivers (hyporheic passive flux meter, HPFM). With HPFMs we directly assessed time-integrated lateral hyporheic nitrate fluxes during early spring and midsummer covering different temperature and discharge regimes. Contrary to our expectations, higher stream discharge coincided with substantially lower hyporheic exchange rates. While in streams featuring a natural morphology, bed form induced exchange commonly increases with surface flow, the influence of groundwater level was dominant in this reach. Furthermore, in contrast to less impacted environments, where progressive substrate depletion with depths reduces metabolic rates in the subsurface, we identified not the upper, but the intermediate layer of the hyporheic zone as hot spot of nutrient turnover. Overall, the hyporheic zone at the study site functioned partly as nitrate source, partly as a sink. Neither of the commonly used determinants redox state and residence time could explain this source or sink function. Our results give clear evidence to carefully transfer the knowledge of hyporheic zone processes from “natural” systems to anthropologically modified streams.