Atmospheric conditions, such as the pressure (P), temperature (T) or air density ($\rho \propto P/T$), affect the development of extended air showers initiated by energetic cosmic rays. We study the impact of the atmospheric variations on the reconstruction of air showers with data from the arrays of surface detectors of the Pierre Auger Observatory, considering separately the one with detector spacings of 1500 m and the one with 750 m spacing. We observe modulations in the event rates that are due to the influence of the air density and pressure variations on the measured signals, from which the energy estimators are obtained. We show how the energy assignment can be corrected to account for such atmospheric effects.