In this work, we explore the implications of using the popular single-station model when interpreting stream oxygen dynamics and performing metabolism-based assessments. To this end, we use a new multiscale model for reactive transport in stream corridors that explicitly represents the net result of in-channel and hyporheic zone processes in whole-stream metabolism. We configure the multiscale reactive transport capability in the Advanced Terrestrial Simulator (ATS) code to represent key processes controlling oxygen dynamics: gross primary production (GPP) and ecosystem respiration (ER) in the channel, oxygen exchange with the atmosphere, hyporheic exchange and advective transport, and aerobic respiration in the hyporheic zone. Numerical experiments with the new multiscale model and Bayesian parameter estimation are used to assess potential biases that may arise from neglecting mass transfer limitations, as is commonly done in the single-station method for estimating GPP and ER from time-resolved oxygen measurements. The insights from this work are critical for interpreting field observations and translating mechanistic understanding into predictive modeling frameworks that capture metabolic processes across river networks.