The most serious degradation factor affecting soil quality in the Czech Republic, as in other countries, is water erosion. This threatens more than 50% of agricultural land. One of the contributing factors to accelerated water erosion is the structure of the agricultural land fund where there was land consolidation in the post-war period and disposal of landscape elements, including greenery. The present fragmented landscape thus forms a mosaic of significantly larger “grain” than it did in the pre-war period. For example, the average size of arable land blocks is now approximately 11 hectares, and this was much lower before World War II. The result is a remarkable decline in biodiversity, bound to the original heterogenous landscape which has disappeared from today’s dull environment. This paper presents a new approach to soil protection solutions while supporting biodiversity in the landscape. It offers a developed method for changes to landscape structure which considers erosion threats and the land’s potential to contribute to preserving both landscape and species biodiversity. Based on raster modelling of erosion processes and landscape connectivity in GIS and Statistics, we propose measures that will reduce the overall risk of erosion and other related degradation changes and increase functional connectivity of the landscape; thus resulting in increased biodiversity in areas of interest.