The analysis of wind and temperature data from Alpnacher See (Switzerland) shows the second vertical mode of the internal (baroclinic) seiche to dominate over the first vertical mode. Resonance with diurnal wind is responsible for the high amplitudes of the second mode. Two different models are used to calculate the periods and velocity distribution of the various modes of the internal seiche. First, as a natural extension of Mortimer’s two‐layer model, the eigenvalues of a three‐layer model for a rectangular basin are calculated analytically. The period of the second vertical mode is found to depend strongly on the thickness of the metalimnion. Second, in order to better represent the vertical structure of the water column, a continuous stratification model is adopted and solved analytically for realistic density profiles. The resulting vertical variation of the horizontal velocity is used to calculate local gradient Richardson numbers (Ri) and relate them to the vertical eddy diffusivity estimated with the temperature microstructure method.