We examined long-term relationships between Cladocera and limnogeological and climate variables in a late Holocene lake sediment sequence to assess cladoceran responses to climate change and reconstruct past climate variations in southern Finland, near the Baltic Sea coast. Elemental composition, organic matter, and inferred water quality variables were used to constrain paleoenvironmental (until 4500 cal BP) conditions and human impact. Fossil Cladocera assemblages, ephippia, and body size trends were utilized to estimate mean July air temperature (T Jul) variability, open-water season length, and water-temperature regimes. Results revealed stable cladoceran communities, dominated by Eubosmina, until 500 cal BP, followed by major assemblage changes including increases in Chydorus cf. sphaericus, Alonella spp., and Bosmina longirostris. Pb and Cu concentrations were associated temporally with increasing human impact and warming climate during the past few centuries, and were the most significant factors in explaining cladoceran community changes, based on redundancy analysis. A Cladocera-based T Jul reconstruction estimated elevated temperatures for the end of the Holocene Thermal Maximum, a cooler period during ~3000–2000 cal BP, slightly increased temperatures during 1200–800 cal BP corresponding to the Medieval Climate Anomaly (MCA), and lower temperatures during the Little Ice Age (LIA), 800–200 cal BP. The reconstruction also suggests that significant climate warming took place during the twentieth century. Cladocerans mostly associated with warm periods included B. longirostris and Pleuroxus uncinatus, whereas Alona affinis, A. quadrangularis, and C. cf. sphaericus were associated with colder climate. Compared to a reference Chironomidae-inferred T Jul reconstruction from the same region, discrepancies were apparent in amplitude of temperature change, as the temperature variability in the cladoceran-based record was muted until ~200 cal BP. During the LIA, increased ephippia and body size agreed with the temperature reconstruction, but suggested a severely shorter open-water season and reduced water temperatures compared to the preceding late Holocene episodes, even though the cladoceran T Jul showed quite similar temperatures for these periods. Our results suggest that fossil cladoceran assemblages, ephippia, and morphological attributes respond sensitively to long-term climate fluctuations and this record reflects well the major climate events of the late Holocene and provides realistic paleoclimatic estimates for maritime southern Finland.