Temperature changes over the Tibetan Plateau (TP) exhibit a dependence on altitude, as observed from meteorological station data and Moderate Resolution Imaging Spectroradiometer (MODIS) land surface temperature (LST) data. However, little is known about the changes in water surface temperature (WST) of lakes in the TP under the warming climate conditions over the past few decades. In this study, lake WST was examined using a MODIS/Terra 8-day LST (nighttime) product (MOD11A2) over the period 2001 − 2012. It was found that 52 lakes included in the analysis of WST exhibited an average rate of change of 0.012 ± 0.033 °C/year. Of these 52 lakes, 31 lakes (60%) displayed a temperature increase with a mean warming rate of 0.055 ± 0.033 °C/year and 21 lakes (40%) displayed a temperature decrease with a mean cooling rate of −0.053 ± 0.038 °C/year. The rates of change in WST for 13 lakes were statistically significant, and these included 9 warming and 4 cooling lakes. Of the 17 lakes with nearby weather stations, 9 lakes (53%) showed faster warming than nearby air/land. The warming lakes could be attributed to locally rising air and land surface temperatures as well as other factors such as the decreased lake ice cover. The cooling lakes were mostly located at high elevations (>4,200 m), and the trend could have been due to increased cold water discharge to the lakes from accelerated glacier/snow melts. Therefore, both warming and cooling lake temperatures in the TP were possibly the result of increased air temperatures (0.036 ± 0.027 °C/year) under global warming conditions.