Scenarios of changes in biodiversity for the year 2100 can now be developed, based on scenarios of changes in atmospheric CO2, climate, vegetation, and land use and the known sensitivity of biodiversity to these changes in terrestrial and freshwater ecosystems. This study identified (1) a ranking of the importance of drivers; (2) a ranking of the biomes with respect to expected changes; and (3) the major sources of uncertainties. For terrestrial ecosystems, land-use change will probably have the largest impact on biodiversity followed by climate change, nitrogen deposition, biotic exchange, and elevated CO2. For freshwater ecosystems, biotic exchange is of much greater importance than in terrestrial ecosystems. Mediterranean-climate and grassland ecosystems will likely experience the greatest proportional change in biodiversity, due to substantial impact of all drivers of biodiversity change. Northern temperate ecosystems are estimated to experience least biodiversity change because major land-use change has already occurred. Plausible changes in biodiversity in other biomes depend on assumptions about the interactions among causes of biodiversity change. These interactions represent one of the largest uncertainties in projections of future biodiversity change.