Abstract The aim of this paper was to present possibilities of using different substrates to assist the bioremediation of soils contaminated with heavy metals, pesticides and other substances. Today's bioengineering offers many solutions that enable the effective conduct of biological remediation, including both biostimulation and bioaugmentation. For this purpose, they are used to enrich various organic substances, sorbents, microbiological and enzymatic preparations, chemical substances of natural origin or nanoparticles. The use of genetic engineering as a tool to obtain microorganisms and plants capable of efficient degradation of pollutants may cause the risks that entails the introduction of transgenic plants and microorganisms into the environment. In order to determine the efficacy and possible effects of the various bioremediation techniques, it is required to conduct many studies and projects on a larger scale than only in the laboratory. Furthermore, it should be emphasized that bioremediation involves interdisciplinary issues and therefore, there is a need to combine knowledge from different disciplines, such as: microbiology, biochemistry, ecology, environmental engineering and process engineering.