Research has shown that many chemicals form persistent and permanently bound residues in soils and sediments that play an important role in soil and sediment detoxification processes, long-term compound partitioning behaviour and compound bioavailability and toxicity in soil and sediment. This article reviews the methodological approaches that have been applied to determine the nature of bound residues in soil and sediment, the application of specific analytical techniques, the type of information they generate, and their relative advantages and disadvantages. It begins by defining bound residues and discussing soil–compound interactions. The application of model compound studies for elucidating specific binding interactions is reviewed along with long-term laboratory and field soil incubation experiments. The use of radiolabelled compounds, isotopically labelled compounds and combinations of both in these experiments are outlined by examples from the literature, along with sequential extraction schemes for releasing bound residues from soil, sediment and humic materials. The importance of spectroscopic methods, and particularly nuclear magnetic resonance techniques for characterising the structure of bound residues in soil and sedimentary humic substances is discussed and illustrated by examples from the literature on the subject. The process of bound residue formation is highly complex and requires further research to establish the mechanisms of bound residue formation and their subsequent environmental and toxicological fate. Much of the uncertainty regarding the elucidation of bound residue formation arises from our poor understanding of the structure of soil and sedimentary organic matter. Significant advances in our understanding of the formation and fate of bound residues will be made when we develop a deeper insight into the complex and heterogeneous structure of soil and sedimentary organic matter.