Equatorial plasma bubbles consist of field‐aligned large‐scale depletions, or irregularities, characterized by drastic ion density rarefactions of the nocturnal low latitude/equatorial ionosphere. Understanding their behavior is important because of their degrading effects on radio wave signals and, consequently, their respective technological applications such as, for example, Global Positioning System applications. In this sense, a methodology of pattern recognition was developed and implemented here using the Long‐Term Ionospheric Anomaly Monitoring in order to infer the plasma bubbles zonal drift velocities, using two receiving stations of global navigation satellite systems data from the Brazilian Continuous Monitoring Network, located near to each other, in Salvador (BA) during geomagnetically quiet periods. The study covered the years of 2012, 2013, and 2014 for the months from September to January of the following year, choosing 10 representative days for each month. The average results for the plasma bubble zonal velocities provided by the model calculations were in agreement with the well‐known values. However, monthly individual analysis showed a behavior anticorrelated with that expected for high solar flux. Probably, the unexpected behavior is due to atypical configuration of the solar activity ascending phase. Key Points Automatic calculation of the plasma bubbles velocities by LTIAM model Using GNSS signals to infer plasma bubbles velocities