GPS tomography has been investigated since 2000 as an attractive tool for retrieving the 3D field of water vapour and wet refractivity. However, this observational technique still remains a challenging task that requires improvement of its methodology. This was the purpose of this study, and for this, GPS data from the Australian Continuously Operating Research Station (CORS) network during a severe weather event were used. Sensitivity tests and statistical cross-comparisons of tomography retrievals with independent observations from radiosonde and radio-occultation profiles showed improved results using the presented methodology. The initial conditions, which were associated with different time-convergence of tomography inversion, play a critical role in GPS tomography. The best strategy can reduce the normalised root mean square (RMS) of the tomography solution by more than 3 with respect to radiosonde estimates. Data stacking and pseudo-slant observations can also significantly improve tomography retrievals with respect to non-stacked solutions. A normalised RMS improvement up to 17% in the 0–8 km layer was found by using 30 min data stacking, and RMS values were divided by 5 for all the layers by using pseudo-observations. This result was due to a better geometrical distribution of mid- and low-tropospheric parts (a 30% coverage improvement). Our study of the impact of the uncertainty of GPS observations shows that there is an interest in evaluating tomography retrievals in comparison to independent external measurements and in estimating simultaneously the quality of weather forecasts. Finally, a comparison of multi-model tomography with numerical weather prediction shows the relevant use of tomography retrievals to improving the understanding of such severe weather conditions.