To determine how differences in geomorphologic setting influence spatial heterogeneity in transport and uptake of limiting nutrients, we investigated reach-scale interactions between porous bed material textures, bed morphology, transient storage, and nutrient retention in a field-scale flume (84 m × 2.75 m). Conservative salt tracer and soluble reactive phosphorous additions were used to quantify effects of plane bed and alternate bar morphologies, and clean gravel versus sandy gravel bed texture on reach-scale nutrient retention and transient storage. We conducted experiments under light and dark conditions to clarify the role of benthic production on surface-subsurface hydrologic interactions and the relative influence of increasing biomass on nutrient uptake rates. Mean water residence time varied by a factor of 8 across treatments (4–32 min) and transient storage volume varied strongly with sediment texture. The exchange rate coefficient was greatly influenced by presence of alternate channel bars. Phosphorus uptake had the tendency to change with total volume of sediment-water interaction during dark conditions where periphyton abundance was low. However, under light conditions, periphyton growth clogged bed material pores and essentially eliminated exchange between the surface and subsurface. Uptake then was related to periphyton biomass accumulation rather than hydraulic or geomorphic parameters. The location and mechanism of stream nutrient retention may be more temporally and spatially dynamic than previously realized. Under clean bed conditions in streams (e.g., shaded riffles, streambeds following floods or in winter), nutrient uptake will be hyporheic dominated. Under high periphyton biomass conditions, nutrient uptake will be elevated in the surface sediments, minimal in the hyporheic, and thus benthic dominated.