Acidification affects all components of biological communities in lakes and streams: microbes, algae, macrophytes, invertebrates, fish amphibians, and other vertebrates that rely on aquatic ecosystems for habitat or food. Mechanisms of effect are both direct (toxic responses to changes in chemistry) and indirect (e.g., expressed through the food chain or caused by changes in habitat), and the responses may be immediate or delayed. In turn, many biological processes, especially microbial processes, can influence surface water acid-base chemistry. Thus, chemical and biological changes are intricately linked and complex, with extensive feedbacks. Research on the effects of acid deposition and acidification on aquatic biota has been ongoing in Europe and North America for over the last 15 years, and many comprehensive reviews have been published. These gaps often have occurred because funding has focused on chemical mechanisms and modeling response of systems rather than in making resource inventories or resolving uncertainties in biological responses to acidification.