The composition of charophyte taxa and their habitat preferences in water bodies of the Artabel Lakes Nature Park were investigated on 15 August 2013 and 13 August 2016. A total of 73 taxa belonging to Conjugatophyceae (Zygnematophyceae) and Klebsormidiophyceae were recorded. The genera Cosmarium (37), Staurastrum (10) and Closterium (7) were most abundant. The partly unexpected presence of certain desmid taxa, i.e., taxa characteristic of eutrophic water, was recorded. Filamentous charophytes were represented by three taxa. The Willis curve for the distribution of species to genera had a trend line of R2 = 0.9123. Bioindication, statistical methods and comparative floristic results show that water in all of the studied lakes was fresh, of low-conductivity, circum-neutral and with little organic pollution. Four groups of lakes were identified as a result of statistical comparison of their environmental and biological variables. Bioindication results can be used as references for future monitoring of the lakes in protection of the species found in the Artabel Lakes Nature Park and can also be included in the National Water Quality Standard System of Turkey.