We present a record of dinoflagellate cyst assemblage composition, abundance, and morphology from the central Baltic Sea, spanning from the late 19th to the early 21st century. Environmental time-series were analyzed in relation to changes in community structure and diversity as inferred from the sediment record, and average summer sea surface salinity (SSS) was reconstructed based on the average process length of Protoceratium reticulatum resting cysts. The reconstructed summer SSS was compared to instrumental data for a critical evaluation of this approach. The most abundant species in this record were P. reticulatum and Biecheleria baltica, and on average ten taxa were identified per sample. The cyst record of B. baltica indicated that although this species has been present in the Gotland Basin at least since the 1880s, its concentrations have increased significantly since the 1980s, possibly linked to eutrophication. Variations in assemblage composition and P. reticulatum cyst morphology reflected patterns of major, instrumentally recorded hydrographic and environmental changes in the Baltic Sea during the past century. The variability in microfossil relative abundances was best explained by the average spring SSS as well as by the average NO3 concentrations during spring and by the combined effects of average summer SSS and NAO index variability. Reconstructed summer SSS and instrumental SSS showed notable differences, depending on the year and function applied for reconstruction. Although roughly reflecting the same patterns, the reconstructed values are offset when compared to instrumental measurements. We put forward suggestions for improvement of the process-length method and recommend using the reconstructed values as an indication of relative changes in past summer sea surface salinity, preferably as part of a multiproxy approach.