Natural organic matter (NOM) is the product of microbial and abiotic decay of plant and animal remains in terrestrial and aquatic ecosystems. On a molecular level, NOM is a complex mixture of organic molecules, of which the vast majority of structures are unknown. By identifying these molecules, our understanding of the many functions of NOM could be greatly enhanced. However, given that they are chromatographically inseparable and number in the thousands, traditional analytical techniques have proven unable to achieve this goal. A promising approach to enumerate functional groups and elucidate molecular structures within NOM is based on a combination of molecular tagging and high resolution spectroscopic techniques, such as nuclear magnetic resonance spectroscopy and mass spectrometry. Molecular tagging involves the selective modification of particular functional groups, inserting nuclei to act as reporters on their surrounding chemical environment. This allows examination of only the tagged molecules within NOM, thereby reducing the complexity of the mixture. In this review, the effectiveness of molecular tagging methods incorporating carbon, silicon, nitrogen, phosphorus, and deuterium into NOM are discussed. Some potential tagging methods which have not yet been applied to NOM are also presented.