An increase in the penetration of metal-based nanoparticles (NPs) into the environment requires an assessment of their ecotoxicity as they impair the critical activity of plants, animals, bacteria, and enzymes. Therefore, the study aimed to observe the effects of metal-based NPs, including copper (Cu), nickel (Ni), and zinc (Zn), on the Cambisols, which cover a significant part of the earth’s soil and play an important role in the biosphere. Metal-based NPs were introduced into the soil at concentrations of 100, 1000, and 10,000 mg/kg. The biological properties of the soil are being investigated as the most sensitive to external contamination. The highest ecotoxicity of the studied pollutants introduced into the soil at the same concentrations was shown by Cu (up to 34%) and Zn (up to 30%) NPs, while Ni NPs showed less (up to 22%). Microbiological (total number of bacteria, Azotobacter sp. abundance) and phytotoxic properties (radish seed germination and length of roots) of Cambisols were more sensitive (22–53%) to pollution by NPs of Cu, Zn, and Ni, while enzymatic activity (catalase and dehydrogenases) showed less sensitivity (14–32%). The present results could be useful for biomonitoring the state of contaminated soils, especially by NPs.