In this paper we present a study of the ionospheric effects of a halo coronal mass ejection (CME) initiated on the Sun on September 20, 1999, and causing the largest magnetic storm during this month on September 22--23, 1999, with the hourly Dst index being -167 nT at ~2400 UT on September 22. The recurrent CME on October 18 caused an even larger magnetic storm on October 22, 1999, with Dst of -231 nT at ~0700 UT. The ionospheric effects of these two major magnetic storms are studied through their effects on a prototype of a Global Positioning System (GPS)-based navigation system called Wide Area Augmentation System (WAAS) being developed by the Federal Aviation Administration for use in the continental United States and their impact on global VHF/UHF communication systems. It is shown that the penetration of transient magnetospheric electric fields equatorward of the shielding region at midlatitudes, which have been well-correlated in the past with rapid changes in the well-known Dst index (or through its recently available high resolution 1-min counterpart the SYM-H index), can cause large increases of total electron content (TEC), TEC fluctuations, and saturated 250-MHz scintillation, and these, in turn, may have significant impacts on WAAS. The local time of Dst changes (and not just Dst magnitude) was found to be very important for WAAS, since the largest effects on TEC are seen near dusk. The prompt penetration of these magnetospheric electric fields all the way to the magnetic equator causes augmentation or inhibition of equatorial spread F. The global ionospheric response to these storms has been obtained from ground-based TEC observations with a GPS network and space-based in situ density and electric field measurements using the Republic of China Satellite-1 (ROCSAT-1) and several Defense Meteorological Satellite Program satellites. These prompt penetration electric fields cause VHF/UHF scintillations and GPS TEC variations at low latitudes in the specific longitude sector for which the early evening period corresponds to the time of rapid Dst variations and maximum Dst phase. The effects of the delayed ionospheric disturbance dynamo and those of decreased magnetospheric convection on postmidnight irregularity generation are shown to be confined to a part of the same longitude range that actively responded to the prompt penetration of electric fields in the early evening sector. ¿ 2001 American Geophysical Union