Accurate discharge measurement is mandatory for any hydrological study. While the “velocity” measurement method is adapted to laminar flows, the “dilution” method is more appropriate for turbulent streams. As most low-gradient streams worldwide are neither laminar nor turbulent, a methodological gap appears. In this study, we demonstrate that the application of the “dilution” method to a low-gradient small stream gives very satisfactory results in addition to revealing surface/subsurface processes. A variety of chemical and isotopic tracers were injected into the stream (anions, fluorescent dyes, and chloride and hydrogen isotopes). We report the first use of 37Cl for stream discharge measurement and show that 37Cl and 2H can be reliably used as quantitative tracers. Discharge uncertainty calculations show that deuterium is the most accurate tracer method used. We also compare the differences in the tailing part of the restitution curves of tracers and investigate the role of transient surface and hyporheic zones in solute transport in light of a simple transport modelling approach. We conclude that isotopic tracers can be used as “environmentally friendly” tracers for discrete stream discharge measurements and that the application of multi-tracers tests in rivers opens the path to a better understanding of surface–subsurface interaction processes.