Based on the waveform data of the Jason-2 altimetry satellite from 2008 to 2013, the editing standard, geophysical correction method, and waveform retracking method for satellite altimeter data were studied using Lake Baikal as a case study. The annual and seasonal time series of the abnormal water level of Lake Baikal were calculated using the waveform retracking data, and the seasonal variation rules of the water level were analyzed. The water level of Lake Baikal in October 2013 was predicted using a combined model and compared with the altimeter-derived water level. The results show that the waveform retracking method improves the measurement accuracy of the water level of Lake Baikal, and this is a feasible method of investigating the variation of water level.