Using data of the vertical sounding ionosonde and the GNSS receiver operating in Irkutsk, we analyzed the correlation of short-period (periods less than 24 hours) wave disturbances of the peak electron density of the F2 layer (NmF2) and the total electron content (TEC) in the ionosphere. The measurement data for the period 2003–2020, which included almost two solar cycles, were processed. It has been established that the most probable case is a high positive correlation of short-period disturbances of NmF2 and TEC. With the growth of solar and geomagnetic activity, the number of cases of strong positive correlation increases (from 53% to 66%) and the number of cases of both positive and negative weak correlation decreases (from 46% to 33%). During powerful geomagnetic storms, the highest correlation (up to R = 0.89) is observed in the storm main phase and then decreases in the recovery phase up to negative R values. Possible physical mechanisms of the obtained results are considered.