In this paper, data from Nigerian Global Positioning System/Global Navigation Satellite System (GPS/GNSS) network (NIGNET) for the year 2012, together with those from surface meteorological stations, National Center for Environmental Prediction (NCEP) Reanalysis II, and the Department of Energy (DOE) Numerical Weather Prediction (NWP) model have been used to estimate the precipitable water vapour (PWV) in three NIGNET stations across Nigeria (i.e., Zaria, Abuja and Lagos). The GPS/GNSS data was analysed using RTKLIB (ver. 2.4.2) open source GPS/GNSS software. This work aims to highlight the importance of GPS PWV in NWP modelling as well as to show that GPS PWV data could be assimilated into NWP models leading to improved weather forecast. The measured PWV by GPS/GNSS was found and compared with NCEP Reanalysis II, with R2 of 0.08, 0.006 and 0.106, RMS error of 0.32 cm, 0.29 cm and 0.99 cm, while the surface meteorological data was also compared, with R2 of 0.114, 0.045 and 0.004, RMS error of 0.34 cm, 0.30 cm and 0.28 cm for Zaria, Abuja and Lagos respectively.