This paper is concerned with the presentation of the methodology to GIS mapping of the territory according to degree of vulnerability to aridification/humidification processes. The methodology is based on combination of different thematic information, such as paleogeographic, landscape, archaeological, geobotanical, with characteristics of the geomorphological framework built by using of the digital elevation model SRTM (Shuttle Radar Topographic Mission). The area under consideration is located on the Baraba Plain, which has close to the surface position of groundwater. The interrelation between the parameters of landscape and moistening (ground and atmospheric) was considered through the concept of automorphic and hydromorphic lands, on the basis of the indicator of relative elevation derived according to a digital elevation model. Two models of vulnerability of the territory were built by using this indicator for four landscapes (with ridges, lakes, ridges and lakes, and plain) for aridification and humidification cases. The obtained results show areas, which are the most vulnerable to activation of exogenic processes dependent on climatic changes. The study concluded that automorphic surfaces are less vulnerable to humidification and more vulnerable to aridification. At the same time, hydromorphic areas of all types of landscape are vulnerable to both humidification and aridification. Thus, aridification is the most dangerous trend for the south of the West Siberian Plain. The novelty of these models is the ability to assess the degree of transformation of terrestrial ecosystems simultaneously over the entire area and locally for each of its sites at the medium-scale level of research. The proposed methodology allows correcting predictive models and paleo-geographic reconstructions depending on landscape features of the territory.