Scintillations caused by ionospheric irregularities during Global Navigation Satellite System (GNSS) measurements are detected and mitigated. Detection is based at least in part on statistical properties of geometry-free combination parameters calculated from input GNSS measurements corresponding to the same navigation satellite and different carrier frequencies. Mitigation is based at least in part on ionosphere-free combination parameters calculated from input GNSS measurements corresponding to the same navigation satellite and different carrier frequencies. Depending on the number of satellites with detected scintillations, different algorithms are used to calculate values of target parameters from a set of ionosphere-free combination parameters or from a set of ionosphere-free combination parameters and the remaining input GNSS measurements. Different algorithms accommodate stand-alone mode code phase measurements, stand-alone mode carrier phase measurements, differential navigation mode code phase measurements, and differential navigation mode carrier phase measurements.