First study of macrophytes and Charophytes of three protected lakes in Donetsk region of Ukraine has been implemented for ecological assessment of the lakes environment by bio-indication methods. Altogether five species of mactophytes and three species of macroalgae were revealed. Rare species Chara dominii Vilh. was found in massive grow in the Flora Lake. The lakes Flora and Molodezhnyy are mesotrophic and low-to middle organic polluted, while the Azotnyy Lake is oligotrophic, low organically polluted. Statistical methods show that organic pollution come mostly from ground waters enriched by mine waters, and together with soluble sodium from surface runoff they are stimulated species growth. Lake Molodezhnyy can be used as referent site for monitoring, whereas the Azotnyy Lake needs more attention in study of toxic substances, and the Flora Lake for organic matter influence. Bio-indication methods together with statistic approaches can be used as sensitive instrument for ecosystem state assessment and watershed protection in the technogenically impacted area such as Donetsk region of Ukraine.