Stream functioning includes simultaneous interaction among solute transport, nutrient processing, and metabolism. Metabolism is measured with methods that have limited spatial representativeness and are highly uncertain. These problems restrict development of methods for up-scaling biological processes that mediate nutrient processing. We used the resazurin—resorufin (Raz-Rru) tracer system to estimate metabolism at different spatial scales (habitat, subreach, and reach) in 2 headwater streams of the H. J. Andrews Experimental Forest (Oregon, USA), and present a mathematical framework for its application. We investigated the relationship between metabolism and hydrodynamics, i.e., geomorphic units (e.g., pool—riffle, pool—cascade), bed materials (i.e., alluvium vs bedrock channels), and type of transient storage (i.e., pure hyporheic exchange, pure surface transient storage, and a combination of both). The metabolic hotspots detected by the Raz-Rru system in both watersheds were related to hydrodynamic conditions known to increase biological processing. Higher respiration rate coefficients were found in subreaches with extensive hyporheic flow and flow through large woody-debris complexes, and higher reaeration rate coefficients were found in subreaches with intensive respiration activity and higher flow velocities. Because such hydrodynamic conditions and their effects on stream processing are difficult to quantify in headwater streams without the use of tracer techniques, the Raz-Rru system proved to be a good integrator of solute transport and stream metabolism processes.