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In the current study, sub-fossil Cladocera collected from the surface sediment of 44 shallow lakes spanning over five latitudes from north to south of Turkey using snap-shot methodology revealed strong impact of salinity on cladoceran community structure. To see the whole picture, sediment cores collected from six of the lakes and long-term monitoring data from two of the lakes were also investigated. Contemporary cladocerans and sub-fossil assemblages were compared to reveal that their responses to salinity changes were highly similar. This lead us to use sub-fossil cladocerans and salinity data from water column together while generating the calibration data set using ordination techniques. Salinity transfer function models were developed utilising weighted averaging techniques. The developed salinity transfer function was applied to cladocera assemblages from dated sediment cores. Hindcasting of the salinity inference model was performed using monitoring data and the reconstructed salinities from two central Anatolian lakes and reflected good linear correlation with the known lake salinity history. This thesis has confirmed that sub-fossil Cladocera is a valuable indicator of historical salinity change and marker for the monitoring of lakes. For the first time, the lake environmental variables and sub-fossil cladoceran species composition from the surface sediments of Turkish shallow lakes were studied and a salinity transfer function was developed to elucidate past salinity change. The approach of the current study has been proven to be reliable while interpreting past salinity conditions. Since monitoring programmes are scarce in Turkey, paleolimnological analyses would be beneficial especially when defining effective restoration strategies.