We report here the data set entitled “Impacts of climate change on organisms in the Mediterranean Sea,” which is the basis for the analysis of impacts of climate change on marine organisms presented by Marbà et al. (2015a). The data is deposited at Digital CSIC, the institutional repository of the Spanish National Research Council, and can be accessed at http://hdl.handle.net/10261/116098 (Marbà et al., 2015b).