Military energetic compounds are common environmental pollutants, contaminating soils and water worldwide. In situ microbial degradation of these compounds may be a positive process that reduces their concentration in the environment without any active human involvement. Nevertheless, assessing the extent of biodegradation processes in situ is challenging, and often cannot be achieved with satisfactory sensitivity using conventional methods. Isotope methods, on the other hand, may be a suitable alternative for assessing these processes. This chapter will focus on the application of compound-specific isotope analysis (CSIA) to study the fate of military energetic compounds in the subsurface, focusing on nitroaromatics, nitramines, and perchlorate. CSIA can also be used to provide an intrinsic mechanistic understanding of the transformation reactions of such compounds and this aspect will be described as well.