We compared the relative influences of biochemical uptake processes and dynamic hydrology and geomorphology (hydrogeomorphology) on molybdate reactive phosphorus (MRP) retention within a stream. MRP concentrations were measured upstream and downstream of a 4.5-km reach undergoing dynamic channel adjustment in response to downstream dam removal. Geomorphic adjustments following removal produced measurable changes in velocity and depth, and decreases in MRP retention. Paired upstream and downstream measurements of MRP concentration were used to compute three retention metrics: uptake rate, mass transfer coefficient, and uptake length, which were used as model parameters. Modeling results showed that changes in channel morphology alone following dam removal could result in an approximate 40% increase in downstream MRP concentrations compared with conditions with the dam in place. However, empirical and modeling results indicate that hydrogeomorphology can control nutrient retention on the reach scale only when uptake processes are either sufficiently great or when uptake rates have limited variability. Review of published phosphorus retention values revealed greater variability in biochemical uptake rates than in hydrogeomorphology. Thus uptake rates should exert a stronger control on reach-scale MRP retention than changing channel morphology or hydrology. These results suggest that maintaining or restoring channel conditions that are conducive to biochemical uptake are of greater priority than restoration of hydrologic or geomorphic conditions alone.