Multi-chronological examination of territory using GIScience and historical cartography may reveal a strategic tool for investigating changes in land use and the surrounding landscape structure. In this framework, the soil plays a key role in ecosystem evolution, since it governs all the mechanisms at the basis of vegetal growth, as well as all components of the total environment contributing to the formation of a rural landscape, including the balance of carbon dioxide. The present study was developed using a GIS approach applied to historical maps and aims to assess the environmental impact of land-use change, with particular attention to its effects on agricultural soil and atmospheric carbon dioxide balance. Thanks to a comparison between historical cartographic maps of different periods, this geospatial approach has enabled the assessment of the evolution of the rural land of the study area in the municipality of Ruoti (Basilicata Region—Southern Italy). This area, indeed, has been affected by deep land-use transformations, mainly caused by agricultural activities, with a resulting impact on the atmospheric CO2 balance. These transformations have been analyzed and quantified in order to contribute to the understanding on how the changes in land use for agricultural purposes have led to unforeseen changes in the rural landscape, ecosystems and the environment. The results showed that the greatest changes in land use were caused by the abandonment of large rural areas, resulting in the expansion of urban areas, a decrease in orchard and arable land (about less 25%), and an increase in woodland (more than 30%). These changes have resulted in a doubling in soil carbon fixation value. The final results have therefore confirmed that historical cartography within a GIS approach may decisively offer information useful for more sustainable agricultural activities, so as to reduce their negative contribution to climate change.