This work presents a novel monitoring method for detecting material loss from the decay inventory of the molten salt breeder reactor (MSBR) by monitoring for changes to the system dynamics using an isotopic ratio. The isotopic masses in the decay inventory of a MSBR were simulated under several material loss scenarios. In each case, the ratio of 231Pa to 233Pa served as a sensitive and lasting indicator of material loss. This isotope ratio quickly decreased outside the normal range after a material loss, and the ratio remained depressed for several years after the loss. The dynamics of this ratio were driven by the periodic batch discard from the decay inventory every 220 days, which was specified in the MSBR design to periodically remove fission product buildup. For this method, isotopic ratios were found to be rapid and enduring indicators of inventory change if they comprise a pair with a short half-life (e.g., 233Pa) and a long half-life (e.g., 231Pa) relative to the effective half-life induced by the driving system process (e.g., the batch discard cycle). Using such an isotope pair enabled a method to monitor for changes to the effective half-life of the system and by extension changes to the system inputs and outputs.