Water vapor column density, or vertically-integrated water vapor (IWV), is monitored by ground-based microwave radiometers (MWR) and ground-based receivers of the Global Navigation Satellite System (GNSS). For rain periods, the retrieval of IWV from GNSS Zenith Wet Delay (ZWD) neglects the atmospheric propagation delay of the GNSS signal by rain droplets. Similarly, it is difficult for ground-based dual-frequency single-polarisation microwave radiometers to separate the microwave emission of water vapor and cloud droplets from the rather strong microwave emission of rain. For ground-based microwave radiometry at Bern (Switzerland), we take the approach that IWV during rain is derived from linearly interpolated opacities before and after the rain period. The intermittent rain periods often appear as spikes in the time series of integrated liquid water (ILW) and are indicated by ILW ≥ 0.4 mm. In the present study, we assume that IWV measurements from radiosondes are not affected by rain. We intercompare the climatologies of IWV(rain), IWV(no rain), and IWV(all) obtained by radiosonde, ground-based GNSS atmosphere sounding, ground-based MWR, and ECMWF reanalysis (ERA5) at Payerne and Bern in Switzerland. In all seasons, IWV(rain) is 3.75 to 5.94 mm greater than IWV(no rain). The mean IWV differences between GNSS and radiosonde at Payerne are less than 0.26 mm. The datasets at Payerne show a better agreement than the datasets at Bern. However, the MWR at Bern agrees with the radiosonde at Payerne within 0.41 mm for IWV(rain) and 0.02 mm for IWV(no rain). Using the GNSS and rain gauge measurements at Payerne, we find that IWV(rain) increases with increase of the precipitation rate during summer as well as during winter. IWV(rain) above the Swiss Plateau is quite well estimated by GNSS and MWR though the standard retrievals are limited or hampered during rain periods.