Spatiotemporal geostatistical analysis of groundwater levels is a significant tool for groundwater resources management. This work presents a valid spatiotemporal geostatistical model for the groundwater level variations of an aquifer in Crete, Greece. The goal of this approach is to accurately map the aquifer level at variable time-steps using joint space–time information. The proposed model applies the space–time ordinary kriging (STOK) methodology using joint space–time covariance functions. A space–time experimental variogram is determined from the monthly groundwater level time-series between the hydrological years 2009 and 2014 at 11 sampling stations. The experimental spatiotemporal variogram is successfully fitted by the product–sum model using a Matérn spatial and temporal function. STOK was used to predict the monthly groundwater level at each sampling station from January to May 2015. Validation results show low prediction errors that range from 0.95 to 1.45 m, while the kriging variance accurately determines the variability of predictions. Maps of groundwater level predictions and uncertainty are developed for significant months of the validation period to assess the aquifer spatiotemporal variability. This work demonstrates that space–time geostatistics can successfully model the spatial dynamic behaviour of an aquifer when the space–time dependencies are appropriately modelled, even for a sparse dataset.