The role of allochthonous organic matter in lotic ecosystems has been an important research topic among aquatic ecologists since the seminal work by Lindeman was published in 1942. Since 1986, studies on organic matter budgets, ecosystem metabolism, and decomposition published in J-NABS have made significant contributions to the overall understanding of organic matter dynamics in streams. In this review, we summarize the utility of organic matter budgets, cover the major advances in research on ecosystem metabolism, and describe the intrinsic and extrinsic factors influencing organic matter decomposition. We also discuss future directions and current applications of research and highlight the need for additional studies on the role of land use and climate change, as well as continued use of organic matter processing as a functional metric in biomonitoring studies. We emphasize the need for continued data synthesis into comprehensive organic matter budgets. Such comparative studies can elucidate important drivers of organic matter dynamics and can assist in the understanding of large continental/global changes that might be occurring now and in the near future. In general, continued emphasis on synthesizing information into a larger framework for streams and rivers will improve our overall understanding of the importance of organic matter in lotic ecosystems.