This research presents an analysis of the frequencies and vibration modes of the structure of the superficial seiches of Lake Chapala using mathematical modelling and measurements. The HAMSOM model was run with wind fields from coastal meteorological stations and for different lake storage levels. The lake water level measurements were carried out in two campaigns in 2003. An analysis of the surface seiches in the lake was performed using the fast Fourier transform method. A spectral analysis of lake water level measurements reveals seiches with periods close to 5.9, 3, 2, and 1.5 h. A comparison with the periods calculated by the HAMSOM model indicates that these periods correspond to superficial seiches of the fundamental longitudinal mode of the lake and the subsequent three modes. The lake has undergone important changes in its storage level over time. Therefore, we modelled it with storage levels from the isobaths 90 to 95 m and found that surface seiche periods decreased to 5.2 h.