Beysehir and Mogan Lakes are two shallow Lakes that are under environmental protection status. Phytoplanktonic dominant algae determined in Beysehir Lake were Oscillatoria sp., Cladophora sp., Achnanthes sp., Gomphonema sp., Navicula sp., Cosmarium sp., Cymbella sp., Fragilaria sp., Oocystis sp., Spirogyra sp., Diatomae sp., Microcystis sp. and Staurastrum sp. While in Mogan Lake, Spirogyra sp., Zygnema sp., Euglena sp., Achnanthes sp., Cymbella sp., Fragilaria sp. Navicula sp., Scenedesmus sp., Oocystis sp., Synedra sp., Oscillatoria sp., Chlorella sp., Cosmarium sp. and Nitzshia sp. were determined. Zooplanktonic dominant organisms determined in Beysehir Lake were Eudiaptomus drieshi, Daphnia longispina and Brachionus calyciforus while Arctodiaptomus sp., Keratella quadrata, Filinia longiseta and Diaphanosoma lacustris were determined in Mogan Lake. Accumulation of heavy metals (Cd, Pb, Hg and Cr) in the water and plankton of Beysehir and Mogan Lakes was studied seasonally, from April 2000 to December 2004. Higher concentration with all heavy metals was recorded in plankton. Mercury (Hg) was found in lowest and lead (Pb) in the highest correlation; however, the concentration of each metal varied seasonally. In addition, the seasonal changes in phytoplankton and zooplankton populations and species abundance were also determined. Some physical-chemical parameters of water and their correlation with heavy metals were also examined.