The resazurin (raz)-resorufin (rru) smart tracer system has led to significant advances in hydrologic and biogeochemical sciences but its application has been limited in scope and geography by the short duration that it has been assumed samples can be reliably stored before analysis. For the first time, we quantify the effects of sample storage duration and temperature on measured raz and rru concentrations in order to identify robust storage protocols. Raz/rru concentrations equivalent to those typically used in field and laboratory applications were prepared in three different mediums (deionized water, groundwater, and surface water). Samples were stored at 20°C, 5°C, and −20°C, representing average room, refrigerator, and freezer temperatures. Analysis of raz/rru concentration changes were conducted systematically during an 84-day period, with higher frequency of analysis in the first 7 d. For samples stored at room temperature, changes of up to 22.6% were observed over the initial 24 h. In contrast, for samples stored in the refrigerator and freezer, changes of up to 8.4% and 6.9% were observed in the same period, respectively. Freezing samples provided the best preservation, yielding a maximum of ~ 10% change after 14 d compared to a maximum of ~ 30% change when cooled. It is generally recommended that raz/rru samples be stored cooled for up to 48 h and frozen for up to 14 d. This offers exciting opportunities to broaden the application of the raz-rru system to undertake measurements in wider geographical (remote) locations and at increased sampling frequencies.