Differential ranging measurements are formed using first ranging measurements from reference GNSS receivers and second ranging measurements from GNSS receivers on a rover, the first and second ranging measurements received from a plurality of GNSS satellites. A main navigation solution and a main protection level (PL) set are computed based on the differential ranging measurements. Ionospheric threat scenarios associated with experiencing severe ionospheric gradients to one or more of the plurality of GNSS satellites are determined. A supplemental navigation solution and a corresponding supplemental PL set for each of the plurality of ionospheric threat scenarios are computed. A maximum PL set is selected based on the main PL set and the supplemental PL sets to form a final PL set that protects the main solution against nominal navigation threats and severe ionospheric threats.