Bionanotechnology provides many new methods and protocols in nanomaterial preparation. One of these special new chemical methods is phytosynthesis. The application of biological processes in living organisms such as bacteria, fungi and higher plants contributes to rapid and easy formation of metallic nanoparticles. These nanoparticles present a promising future in heterogeneous catalysis and medicine, and here we focus on phytosynthesis of Ag, ZnO and ZrO₂ nanoparticles using leachate from the linden plant. Nanoparticle activity in liquid is an important aspect of their behavior, and we investigated nanoparticles ζ-potential and monitored their particle size by dynamic light scattering during the period of three months. Transmission electron microscopy then determined shape and morphology, with results confirming their spherical shape and average size in tens and hundreds of nanometers. The amount of metals was estimated in tens of mg L-1 and the different nanoparticle sizes obtained by dynamic light scattering and transmission electron microscopy are discussed. The nanoparticles were tested against 4 human pathogens using minimum inhibitory concentration to investigate their antimicrobial potential. Only Ag nanoparticles provided antibacterial properties against Escherichia coli and Pseudomonas aeruginosa; with the remaining nanoparticles having no antibacterial effect on the four tested pathogens. All studied phenomena are related to nanoparticle concentration and their surface charge, and therefore ζ-potential and other physical and chemical properties are important in ascertaining positive and negative aspects of metallic nanoparticles in future applications and related research.