The mesoscale variability of water vapour (WV) in the troposphere is a highly complex phenomenon and modelling and monitoring the WV distribution is a very important but challenging task. Any observation technique that can reliably provide WV distribution is essential for both monitoring and predicting weather. The global navigation satellite system (GNSS) tomography technique is a powerful tool that builds upon the critical ground-based GNSS infrastructure (e.g. Continuous Operating Reference Station – CORS – networks) that can be used to sense the amount of WV. Previous research shows that the 3-D WV field from GNSS tomography has an uncertainty of 1 hPa. However, all the models used in GNSS tomography heavily rely on a priori information and constraints from non-GNSS measurements. In this study, 3-D GNSS tomography models are investigated based on a limited constrained approach – i.e. horizontal and vertical correlations between voxels were not introduced, instead various a priori information were added into the system. A case study is designed and the results show that proposed solutions are feasible by using a robust Kalman filtering technique and effective removal of linearly dependent observations and parameters. Discrepancies between reference wet refractivity data derived from the Australian Numerical Weather Prediction (NWP) model (ACCESS) and the GNSS tomography model using both simulated and real data are 4.2 ppm (mm km⁻¹) and 6.2 ppm (mm km⁻¹), respectively, which are essentially in the same order of accuracy.