Ecologists have long used observations of assemblage composition to infer environmental conditions at a site. These inferences rely on the notion that different organisms require particular environmental conditions to persist. In recent years, the increased availability of large datasets and the development of new statistical methods have enhanced the accuracy and general applicability of biological inferences. Thus, biological inferences have become increasingly important for addressing environmental and ecological questions. In this session we survey recent methodological developments in biological inference. We also consider how biological inferences have been used to answer environmental questions, such as determining historical environmental conditions and setting restoration targets, assessing the biological condition of different ecosystems, and diagnosing the causes of degradation.