These data were generated to investigate important determinants of the relative abundance of most dominant zooplankton groups in Fennoscandian (Sweden and Finland) lakes. The data were build using archives of temperature, water chemistry and zooplankton data from 60 Scandinavian lakes that represent broad spatial and temporal gradients in key parameters: temperature, calcium (Ca), total phosphorus (TP), total organic carbon (TOC), and pH. The results of the study are presented in paper titled "Declining calcium concentrations drives shifts toward smaller and less nutritious zooplankton in northern lakes" in Global Change Biology journal. The Swedish data are from the monitoring programs Trend lakes and IKEU commissioned by Swedish Agency for Marine and Water where raw data are hosted at the Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Science (open access at: https://miljodata.slu.se/MVM). The Norwegian data are from a national inventory of lakes with a trend lake monitoring program on a subset of lakes financed by the Norwegian Environment Agency were raw data is hosted at the Norwegian Institute for Water Research.