We compare the capability of ground penetrating radar (GPR) and time domain reflectometry (TDR) to assess the temporal development of spatial variation of surface volumetric water content. In the case of GPR, we measured surface water content with the ground wave, which is a direct wave between the sender and receiver through the upper centimeters of the soil. Spatial water content variation was measured on 18 d with GPR and TDR during a 30-d monitoring period. To ensure large fluctuations in the spatial water content variation, we created a heterogeneous pattern of water content by irrigation on 2 d. The temporal development of the spatial variation was studied by means of the variogram and interpolated water content maps. To compare GPR and TDR variograms, we estimated confidence intervals of the experimental variograms and the variogram model parameters with a jackknife approach and a first-order approximation of model parameter uncertainty. The results showed that the 95% confidence intervals of the GPR experimental variogram were one to two orders of magnitude smaller than the 95% confidence intervals of the TDR experimental variogram because of the larger number of GPR measurements. Consequently, the uncertainty in the variogram model parameters was also much lower for GPR, which meant that the temporal development of the fitted GPR variogram model parameters was easier to interpret. Furthermore, the larger GPR measurement volume resulted in a low spatial nugget variance of 1 × 10−6 to 1 × 10−9 (m3 m−3)2 because short distance variation was averaged. This meant that GPR accurately measured spatial correlation lengths, even in the case of low water content variation. Interpolated maps showing the increase of water content due to irrigation and the subsequent gradual drying of the soil were more accurate and reproducible for GPR. It was concluded that the noninvasive GPR measurements provide the means to accurately and consistently monitor the development of spatial water content variation in time.