ZnO, TiO2 and SiO2 nanomaterials were prepared by chemical syntheses and tested for the antimicrobial activity. The phase composition and micromorphology of powder samples were evaluated with the use of XRD and TEM methods. The nanomaterial aqua suspensions with concentrations in the range from 0.01 to 0.25% were prepared and their bactericidal properties were evaluated by interaction with eight types of microorganisms most commonly affecting building materials: Bacillus subtilis, Aspergillus niger, Aspergillus terreus, Aureobasidium pullulans, Cladosporium cladosporioides, Penicillium ochrochloron, Trichoderma viride, Paecilomyces variotii. It is established that ZnO nanoparticles (particle size 2–7 nm) at a suspension concentration varying from 0.01 to 0.25% are the most efficient. In the interaction of microorgamisms with ZnO nanoparticle suspensions, the concentration of microorganisms decreases by 2–3 orders of magnitude depending on their type. The TiO2 and SiO2 nanoparticles demonstrated their low bactericidal activity in the day sun light. The results are promising for the application of ZnO nanomaterials in the creation of building materials and protective coatings that are resistant to biodeterioration.