This study established the hydrochemistry and stable isotope variations in three lakes, namely brackish Zigetang Co, freshwater Cona and Ranwu lakes located in the central and southeastern Tibetan Plateau of China. Vertical profile fluctuations in the water column, such as temperature and dissolved oxygen (DO) concentration, displayed significant differences which were linked to the thermocline. The hydrochemistry of the three lakes showed that as the dominant anion, whereas Na+ is the main cation in Zigetang Co and Cona lake and Ca2+ is the prevailing cation in Ranwu lake. In Zigetang Co, K+ and Na+ concentrations decreased by 42% from 1999 to 2012, caused by the enlargement of the lake area, documented by field investigations carried out in 1998, 2002, 2006 and 2012. The C-13(DIC) and O-18(H2O) values analysed from the three lakes varied from -6.0 to 2.0 parts per thousand, and from -14.8 to -6.4 parts per thousand, respectively. The closed Zigetang lake showed higher C-13(DIC) and O-18(H2O) values compared to those of the rivers, the semi-closed Cona and open Ranwu lakes. The C-13(DIC) values of lake water in Zigetang Co were mainly controlled by CO2 exchange between lake water and atmosphere; the O-18(H2O) values were dominated by the evaporation/freshwater input ratios.