The potential temporal shifts in the integrated water vapor (IWV) time series obtained from reprocessed data acquired from global navigation satellite systems (GNSS) were comprehensively investigated. A statistical test, the penalized maximal t test modified to account for first-order autoregressive noise in time series (PMTred), was used to identify the possible mean shifts (changepoints) in the time series of the difference between the GPS IWV and the IWV obtained from the European Centre for Medium-Range Weather Forecasts (ECMWF) interim reanalysis (ERA-Interim) data. The approach allows for identification of the changepoints not only in the GPS IWV time series but also in ERA-Interim. The IWV difference time series formed for 101 GPS sites were tested, where 47 of them were found to contain in total 62 changepoints. The results indicate that 45 detected changepoints were due to the inconsistencies in the GPS IWV time series, and 16 were related to ERA-Interim, while one point was left unverified. After the correction of the mean shifts for the GPS data, an improved consistency in the IWV trends is evident between nearby sites, while a better agreement is seen between the trends from the GPS and ERA-Interim data on a global scale. In addition, the IWV trends estimated for 47 GPS sites were compared to the corresponding IWV trends obtained from nearby homogenized radiosonde data. The correlation coefficient of the trends increases significantly by 38% after using the homogenized GPS data.