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Hydrologic interactions among biogeochemically active stream subsystems affect material export downstream. We combined a conservative tracer addition with measurements of water table elevation and nutrient concentrations of surface and subsurface water to examine hydrologic interactions among surface and subsurface subsystems and their implications for stream biogeochemistry. We injected bromide ( Br-) into a 400- m reach of Sycamore Creek, a losing stream in central Arizona, for 15 d and monitored changes in concentration in three subsystems: surface, parafluvial, and riparian zones. Additionally, we collected water samples from these subsystems for nutrient analyses. Water flowed from surface to subsurface zones as expected in this losing stream, but a significant amount of subsurface water ( 17% of surface discharge in the reach) returned to the surface. Within the parafluvial subsystem, median transport time (T-med) in two gravel bars differed substantially ( from 2 to 30 h and from 6 to > 300 h, respectively, for upper and lower bars), and varied significantly with depth in the lower bar ( mean ( +/- se) Tmed = 190 +/- 20 h at 30 cm compared to 101 +/- 18 h at 110 cm). Flow paths from the surface to parafluvial and riparian zones, and subsequently back to the surface stream, differ from patterns in mesic areas, where water moves laterally and vertically towards the surface stream. Estimates of nutrient retention for the stream reach varied four fold in response to simulated changes in lateral subsurface connections and the configuration of subsystems. Thus at this scale, accurate nutrient budgets require an understanding of surface-subsurface connections and hydrologic parameters.