Homogenization is an important and crucial step to improve the usage of observational data for climate analysis. This work is motivated by the analysis of long series of GNSS Integrated Water Vapour (IWV) data which have not yet been used in this context. This paper proposes a novel segmentation method that integrates a periodic bias and a heterogeneous, monthly varying, variance. The method consists in estimating first the variance using a robust estimator and then estimating the segmentation and periodic bias iteratively. This strategy allows for the use of the dynamic programming algorithm that remains the most efficient exact algorithm to estimate the change-point positions. The statistical performance of the method is assessed through numerical experiments. An application to a real data set of 120 global GNSS stations is presented. The method is implemented in the R package GNSSseg that will be available on the CRAN.