This study investigates the sensitivity of the GNSSseg segmentation method to change in: GNSS data processing method, length of time series (17 to 25 years), auxiliary data used in the integrated water vapor (IWV) conversion, and reference time series used in the segmentation (ERA-Interim versus ERA5). Two GNSS data sets (IGS repro1 and CODE REPRO2015), representative of the first and second IGS reprocessing, were compared. Significant differences were found in the number and positions of detected change-points due to different a priori ZHD models, antenna/radome calibrations, and mapping functions. The more recent models used in the CODE solution have reduced noise and allow the segmentation to detect smaller offsets. Similarly, the more recent reanalysis ERA5 has reduced representativeness errors, improved quality compared to ERA-Interim, and achieves higher sensitivity of the segmentation. Only 45–50% of the detected change-points are similar between the two GNSS data sets or between the two reanalyses, compared to 70–80% when the length of the time series or the auxiliary data are changed. About 35% of the change-points are validated with respect to metadata. The uncertainty in the homogenized trends is estimated to be around 0.01–0.02 kg m−2 year−1.