We propose the experimental use of resazurin (Raz) and develop a metabolically active transient storage (MATS) model to include processes that may provide additional information on transient storage from a biogeochemical perspective in stream ecosystems. Raz is a phenoxazine compound that reduces irreversibly to resorufin (Rru) in the presence of aerobic bacteria. Raz was added as a stream tracer to a 128‐m reach of the forested second‐order Riera de Santa Fe del Montseny (Catalonia, NE Spain), along with a conservative tracer, NaCl. Raz was transformed to Rru at a rate of 0.81 h−1 in the hyporheic zone and only at a rate of 9.9 × 10−4 h−1 in the stream surface channel. Raz transformation and decay and Rru production and decay were both correlated with O2 consumption measured at wells. The ratio of Raz to Rru concentration at the bottom of the reach was moderately correlated with instantaneous rates of net ecosystem production (NEP) measured over the whole reach. Data for Raz, Rru, and chloride were well fitted with the MATS model. The results from this study suggest that Raz transformation to Rru can be used as a “smart” tracer to detect metabolic activity, specifically aerobic respiration, associated with transient storage zones in stream ecosystems. Therefore, the Raz‐Rru system can provide an assessment of the amount of transient storage that is metabolically active, an assessment that complements the physical characterization of transient storage obtained from conventional hydrologic tracers. The use of both physical and metabolic parameters of transient storage obtained with these tracers may increase our understanding of the relevance of transient storage on stream biogeochemical processes at whole reach scale, as well as the contribution of the different transient storage compartments to these processes.