A method for processing, by a control and computing system of a navigation receiver (122, 200) included in a rover and operating in a differential navigation mode, global navigation satellite system, GNSS, measurements (103A-103F), the method comprising the steps of: generating a first input GNSS measurement difference corresponding to a navigation satellite and corresponding to a first carrier frequency and generating a second input GNSS measurement difference corresponding to the navigation satellite and corresponding to a second carrier frequency, wherein the second carrier frequency is different from the first carrier frequency (402, 502); calculating a geometry-free combination parameter based at least in part on the first input GNSS measurement difference, the second input GNSS measurement difference, the first carrier frequency, and the second carrier frequency; and determining, based at least in part on the geometry-free combination parameter, whether a scintillation caused by an ionospheric irregularity has occurred; wherein: the first input GNSS measurement difference corresponding to the first carrier frequency is based at least in part on first code phase pseudo-range measurements on the first carrier frequency of a first navigation signal, and the first navigation signal is transmitted from the navigation satellite (102A-102F) and received by the navigation receiver of the rover and received by a second navigation receiver in a base station; the second input GNSS measurement difference corresponding to the second carrier frequency is based on second code phase measurements on the second carrier frequency of a second navigation signal, and the second navigation signal is transmitted from the navigation satellite and received by the navigation receiver in the rover and received by the second navigation receiver in the base station; and the geometry-free combination parameter is calculated from the equation (Equation): GFC = Δ D 1 − Δ D 2 / 1 − μ. wherein: GFC represents the geometry-free combination parameter; Δ D 1 represents the first code phase pseudo-range difference between the base and the rover at the first carrier frequency Δ D 2 represents the second code phase pseudo-range difference between the base and the rover at the second carrier frequency; μ = f 1 2 / f 2 2; f 3 represents the first carrier frequency; and f 2 represents the second carrier frequency. generating a first input GNSS measurement difference corresponding to a navigation satellite and corresponding to a first carrier frequency and generating a second input GNSS measurement difference corresponding to the navigation satellite and corresponding to a second carrier frequency, wherein the second carrier frequency is different from the first carrier frequency (402, 502); calculating a geometry-free combination parameter based at least in part on the first input GNSS measurement difference, the second input GNSS measurement difference, the first carrier frequency, and the second carrier frequency; and determining, based at least in part on the geometry-free combination parameter, whether a scintillation caused by an ionospheric irregularity has occurred; wherein: the first input GNSS measurement difference corresponding to the first carrier frequency is based at least in part on first code phase pseudo-range measurements on the first carrier frequency of a first navigation signal, and the first navigation signal is transmitted from the navigation satellite (102A-102F) and received by the navigation receiver of the rover and received by a second navigation receiver in a base station; the second input GNSS measurement difference corresponding to the second carrier frequency is based on second code phase measurements on the second carrier frequency of a second navigation signal, and the second navigation signal is transmitted from the navigation satellite and received by the navigation receiver in the rover and received by the second navigation receiver in the base station; and the geometry-free combination parameter is calculated from the equation (Equation): GFC represents the geometry-free combination parameter; Δ D 1 represents the first code phase pseudo-range difference between the base and the rover at the first carrier frequency Δ D 2 represents the second code phase pseudo-range difference between the base and the rover at the second carrier frequency; μ = f 1 2 / f 2 2; f 3 represents the first carrier frequency; and f 2 represents the second carrier frequency.