Despite the advent of new in silico methodologies to characterize exposure and pharmacokinetic properties of environmental chemicals, numerous limitations remain in the understanding and predicting of metabolic processes. Metabolomics has arisen as means to better inform underlying mechanisms of metabolism and biological effects following chemical exposure. Metabolomics is applied for numerous purposes, including clinical diagnoses of disease, biomarker discovery, toxicological studies, and environmental monitoring. One of the primary challenges involved in metabolomics is identification of detectable metabolites, due to lack of chemical information in databases or reference spectra. Several computational tools, such as metabolite-predicting software and in silico spectral libraries, have been developed to address such issues. Herein, application of such tools is discussed to support environmental monitoring and nontargeted chemical analyses or approaches that are based on pathway frameworks designed to better inform chemical effects within living systems. As these tools advance over time and are able to provide more accurate prediction of metabolites, the list of identifiable chemicals within a given exposure medium will continue to grow. This, in turn, will improve confidence in exposure-based and hazard-based decision-making practices.