Ionospheric anomaly is one of the major error sources which deteriorate the GNSS performance. In the equatorial region, effects of the ionospheric plasma bubbles are of great interest because they are pretty common phenomena, especially in the period of the high solar activity. In order to evaluate the GNSS performance under circumstance of the bubbles, an ionospheric scintillation monitor has been developed and installed in Bangkok, Thailand. Furthermore, a model simulating the ionospheric delay and scintillation due to the bubbles has been developed. Based on these developments, the effects of the simulated plasma bubbles are analyzed and their agreement with the real observation is demonstrated. An availability degradation of the GPS ground based augmentation system (GBAS) caused by the bubbles is exampled in details. Finally, an integrated GPS/INS approach based on the Doppler frequency is proposed to remedy the deterioration.