Inland excess water (IEW) is a form of surplus surface water, often regarded as a specific flood type. However, it occurs most frequently in local depressions of large flat areas, irrespective of river floods and the surface water networks. IEW is considered to be a typical Carpathian Basin problem, as it can cause major land degradation problems in the agricultural areas of Hungary, mainly located on the Great Hungarian Plain (GHP). An innovative method for mapping the probability of IEW inundation is proposed in this study. This method is based on the geostatistical modelling of the relationship between the natural and human driving factors and the occurrence of IEW inundations. The results show that significant part of the GHP (about 500,000 hectares) is moderately or highly affected by IEW inundations, where the combination of multiple influencing factors simultaneously occur. The resulted IEW inundation probability map can be used to meet future challenges in agricultural management and the adaptations to climate change effects.