The high Arctic is in a rapid transition due to climate change, and both direct effects due to warming and an extended growing season, as well as an indirect effect caused by increased bird activity and density (notably geese), strongly affect ponds and lakes. Our study presents the hitherto most comprehensive data on invertebrate freshwater diversity at Svalbard and had three main purposes: to provide a current “baseline” of community composition, to compare current species distribution and occurrence with older data to identify changes that have already occurred, and finally to identify how diversity and community composition are related to the age of localities. To address these aims, we conducted a survey of freshwater invertebrates in 75 ponds and lakes at Svalbard in August 2014 and 2015. We provide a full report of the species’ inventory data for zooplankton, benthos, and meiofauna. We also provide data for species that have likely colonized the sites over the previous decades. Finally, our study also clearly demonstrates a diversity gradient related to ecosystem age and/or parameters confounded with age (e.g., productivity), which may hint at the rate of colonization over the time span from the oldest to the youngest localities.