Acoustic travel time series from an array of nine inverted echo sounders deployed along the equator and in the North Equatorial Countercurrent (NECC) are decomposed into Empirical Orthogonal Functions (EOF) to analyze the dominant frequencies of oscillations in the thermocline field. At low frequencies the first EOF mode describes the seasonal signal, shows the reversal of the NECC and separates the behavior of the Gulf of Guinea from the rest of the basin. The second EOF mode shows rapid changes in the depth of the thermocline in short periods of time on the equator at 10¿W and at 3¿N 38'W. Comparison with a simulation model by Philander and Paconowski shows that the theoretical time series behave in a similar way at these two locations. At high frequencies the modes show oscillations in the inertia-gravity wave band.