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The current study introduces comprehensive insights into the dynamic of phytoplankton community and its consequences on the drinking water. The study also indicated that although the concentration levels of microcystin-LR in drinking water are compatible with the world health organization (WHO), little changes in some physico-chemical parameters of drinking water resources may maximize these levels by stimulating harmful algal blooms. Finally, the current study presents a cost effective method that could be applied to eliminate microcystin-LR in treatment strategies of drinking water.