McClanahan has been working principally on coral reef ecology, most notably for the western Indian Ocean region (especially the African coast and Kenya), including interdisciplinary work about the effects of human activity like fishing on marine ecosystems. He has published over 200 articles in peer-reviewed journals, thirty book chapters, edited four books, compiled seven symposium papers, and produced numerous other publications including popular articles, editorials, and book reviews. According to an evaluation by the International Scientific Information that summarizes the scientific literature, he is the second most cited coral reef scientist in the past 10 years.