Environmental metabolomics can be described as the study of the interactions of living organisms with their natural environments at the metabolic level. Until recently, nuclear magnetic resonance (NMR) spectroscopy has been the primary bioanalytical tool for measuring metabolite levels in this field. While NMR has some specific advantages, the higher sensitivity offered by mass spectrometry (MS) is beginning to revolutionise our ability to probe environmental metabolomes. This review provides the first comprehensive overview of the use and capabilities of MS within environmental metabolomics. Its primary aims are to introduce environmental scientists to the range of MS approaches used in metabolomics and to highlight the breadth and diversity of environmental and ecological research conducted, from ecophysiology and ecotoxicology to chemical ecology. The review is structured around MS approaches: non-targeted gas chromatography-MS, non-targeted directed infusion MS, and both non-targeted and targeted liquid chromatography-MS. Each section begins with a brief introduction to the analytical method, including some advantages and limitations in the context of metabolomics research, and then exemplifies the use of that technique in environmental metabolomics. The review concludes with a discussion on some of the challenges that remain in MS based environmental metabolomics and provides recommendations for the path ahead.