High-frequency variability of the ionospheric Total Electron Content (TEC) can strongly affect precise positioning with GNSS. The occurrence rate as well as the amplitude of such disturbances has been extensively studied over the last decade. Mainly, one can distinguish disturbances due to space-weather events and the others, qualified as “quiet-time” as they are observed during quiet geomagnetic conditions. The latter, which represent more than 75% of the total number of disturbances over mid-latitudes, are then divided into two categories: the Winter Daytime (WD) and the Summer Nighttime (SN). The first category, representing the bulk of quiet-time disturbances, corresponds to classical Medium-Scale Traveling Ionospheric Disturbances (MSTIDs), that are the result of the interaction of gravity waves and the ionospheric plasma. On the other hand, SN disturbances are generally understood as non-classical MSTIDs of electrical origin. The paper investigates the origin of these two types of disturbance based on GPS measurements, ionospheric soundings and wind speed data at a tropospheric level. If one cannot exclude the solar terminator as a potential source of gravity waves responsible for WD events, it is thought that the major contribution comes from the lower atmosphere. More precisely, tropospheric jetstream is considered as the favorite candidate for daytime MSTIDs. Turning to SN disturbances, our analysis reveals that they are related to spread-F phenomenon, linked to the appearance of sporadic E-layers. The related instabilities are responsible for field-aligned irregularities in the F-region, which are thought to be responsible for noise-like fluctuations of the GPS TEC observed during SN events.