Stream fluvial geomorphic structure establishes patterns of surface water and subsurface head distributions, often driving hyporheic exchange through steps, riffles, and meanders. Exchanges of stream water through hyporheic zones provide substrate for hyporheic biogeochemical transformations (e.g. denitrification). In this study, stream tracer experiments and topographic surveys were performed on three streams, one agricultural stream, one urban stream, and one pristine stream, to investigate the control of stream fluvial geomorphic structure on water residence time distributions and nitrate cycling in relation to land use. Urban and agricultural streams had very little streambed elevation variation (near constant slopes along thalwegs), and very short conservative tracer residence time distributions with average reach residence times of 8.53 and 31.41 s/m stream length. The pristine stream had a much more complex geomorphic structure with several riffles, pools, steps and splits. Consequently, the pristine stream residence time distribution was longer (average residence time was 79.03 s/m), indicating greater transient storage within this reach. The results of this study suggest that land-use influences upon fluvial geomorphic structure directly impact transient storage processes and nitrate cycling in streams.