The Institute of Soil Biology and Biogeochemistry of the Biology Centre CAS was established by merging the Institute of Soil Biology and the SoWa Research Infrastructure.

The Institute of Soil Biology was established on 1 January 1986 from the Soil Biology Laboratory, which had been working within the former Institute of Landscape Ecology of the Czechoslovak Academy of Sciences since 1979. The Institute develops the multidisciplinary field of soil biology, i.e. soil zoology, microbiology, chemistry and micromorphology, and addresses fundamental issues related to soil formation, fertility and regeneration. The activities of the Institute are mainly focused on research on the structure and dynamics of soil organism communities in natural and anthropogenically influenced ecosystems, on research on interactions between soil animals, microorganisms and abiotic components of the soil environment, on research on the role of soil organisms in the formation of soil microstructure, on research on humus formation and its transformation and on research on the cycling of biogenic elements in soil.

The SoWa Research Infrastructure was established in 2016 to support research activities and Open Access services aimed at understanding the mechanisms and processes responsible for key ecosystem processes and services aimed at studying the interactions of biotic and abiotic processes responsible for nutrient cycling in soil, aquatic ecosystems and in the transition zones that form the soil-water interface, from the micro to the catchment level. Particular attention was paid to ecosystems under strong anthropogenic pressure, such as areas affected by coal mining.

Since 1 July 2022, the Institute of Soil Biology and Biogeochemistry is part of the Biology Centre CAS in České Budějovice.