Cladocerans are increasingly used in palaeolimnological studies as their community composition is sensitive to both anthropogenic and natural forces in lakes. We present the results of a palaeolimnological investigation of three Turkish shallow lakes located in cold dry steppe and semi-dry Mediterranean climatic regions. The aim was to elucidate historical changes in environmental conditions by analysing sub-fossil cladocerans in ²¹⁰Pb-dated sediment cores. Sub-fossil cladoceran remains from the surface sediment of 40 Turkish lakes were analysed to examine the environmental factors that most correlated with variation in the cladoceran assemblage. Redundancy analysis showed that salinity, macrophyte abundance, fish density, depth and total phosphorus were the most correlated with change in cladoceran assemblage composition with eigenvalues for the first and the second axes being λ₁ = 0.312 and λ₂ = 0.061, respectively. Sedimentary cladoceran assemblages from three cores were placed passively within the framework of the surface sediment ordination. The results reveal a prevalent impact of salinity, fish abundance and water level changes from the past to present. Thus, using cladoceran-based inferences, we traced key environmental changes related to variation in climate change, restoration and water level regulation over the last century.