This textbook provides a unique and thorough look at the application of chemical biomarkers to aquatic ecosystems. Defining a chemical biomarker as a compound that can be linked to particular sources of organic matter identified in the sediment record, the book indicates that the application of these biomarkers for an understanding of aquatic ecosystems consists of a biogeochemical approach that has been quite successful but underused. This book offers a wide-ranging guide to the broad diversity of these chemical biomarkers, is the first to be structured around the compounds themselves, and examines them in a connected and comprehensive way. This timely book is appropriate for advanced undergraduate and graduate students seeking training in this area; researchers in biochemistry, organic geochemistry, and biogeochemistry; researchers working on aspects of organic cycling in aquatic ecosystems; and paleoceanographers, petroleum geologists, and ecologists.