Hyporheic zone reaction rates are highest just below the sediment-water
interface, in a shallow region called the benthic biolayer. Vertical
variability of hyporheic reaction rates leads to unexpected reaction
kinetics for stream-borne solutes, compared to classical model
predictions. We show that deeper, low-reactivity locations within the
hyporheic zone retain solutes for extended periods, which delays
reactions and causes solutes to persist at higher concentrations in the
stream reach than would be predicted by classical approaches. These
behaviors are captured by an upscaled model that reveals the fundamental
physical and chemical processes in the hyporheic zone. We show how time
scales of transport and reaction within the biolayer control solute
retention and transformation at the stream scale, and we demonstrate
that accurate assessment of stream-scale reactivity requires methods
that integrate over all travel times.