New legislation emphasizes the importance of proper disposal of the residues of plant protection products in farms in the agricultural and horticultural sector, because some of those residues may remain in soil in unchanged form for several years, thus affecting the biodiversity of soil microorganisms. A questionnaire survey was conducted to determine the methods of application and disposal of plant protection products by professional users. Biodiversity of microbial communities in soil at sites contaminated by xenobiotics from point sources was evaluated in a laboratory experiment. The awareness of the users of plant protection products regarding responsible and safe use of approved sprayers and the need to train persons performing protective treatments was satisfactory. However, the respondents demonstrated a low level of environmental awareness, and they often declared that in their farms the residues of plant protection products are disposed of in the same place repeatedly. Such practices reduce the biodiversity of soil-dwelling microbes, in particular, the counts of nitrogen-fixing bacteria. In most cases, fungi of the genus Mucor and the species of Fusarium culmorum and Gliocladium roseum did not respond to the presence of the residues of plant protection products in soil.