An increasing number of organic and inorganic pollutants are being detected in the marine environment, posing a severe threat to the ecosystem and human health, even in trace concentrations. Isotope ratio mass spectrometry (IRMS) is one of the critical methods for determining the origin and fate of environmental pollutants and characterising their transformation processes. It has been used for a relatively long time for ecological monitoring of some well-studied industrial hydrocarbons at contaminated sites. However, the method still faces many analytical challenges. This review provides a comprehensive overview of recent technical advances concerning IRMS analysis of various contaminants and discusses typical pitfalls encountered in marine environment analysis. Particular attention is given to the study of sampling techniques and sample preparation for examination, often the keys to successful research given the complexity of marine matrices and the diverse and numerous nature of contaminants. Prospects for developing IRMS to monitor pollution sources and pollutant transformation in the marine environment are outlined.