Lakes Baikal and Balkhash are two of the world’s major lakes affecting fresh water supplies in their catchments. Measurements from satellite altimetry (TOPEX/Poseidon, Jason-1 and -2), satellite gravimetry (GRACE) and a hydrological model (LDAS) are used to see the relationship between lake level change (LLC) and water storage change in these two lakes. At Lake Baikal, the average rate of LLC is negative for 1992 - 1998 and positive for 1998 - 2007, and the reversal of the LLC trend concurs with that of the temperature trend during the 1997 - 1998 El Niño. The rate of gravity change ranges from -0.5 to 0.5 μgal yr-1 with a low over the Tian Shan and a high over western Lake Baikal. Due to the climates over the two lakes, the phases of the annual gravity changes differ by up to 100 days. Using the rates of LLC and gravity changes, the ratios between the mass changes of the lake and its catchment over Lakes Baikal and Balkhash are estimated to 0.6 and 0.3, respectively. The result may help to establish water balance models over these two lakes.