A system and method generates a phase scintillation map that is utilized to de-weight satellite signal observations from GNSS satellites. One or more base stations each assign an index value to one or more GNSS satellite in view, where the index value indicates an adverse effect of ionospheric scintillation on signals received from the GNSS satellite. The values and identifiers may be transmitted to a server. The server utilizes the received information to generate the phase scintillation map that may include one or more scintillation bubbles, wherein a location of each scintillation bubble is based on the received information. The phase scintillation map is transmitted to one or more rovers. The rover determines if a pierce point associated with a selected GNSS satellite in view of the rover falls within the boundaries of a scintillation bubble. If so, satellite signal observations from the selected GNSS satellite are de-weighted.