Work on the investigation of organisms of ballast water and sediments of ships sailing on Russia-Japan and Russia-China lines was started in the Port of Vladivostok for the first time for the Far East seas of Russia. In total, 145 taxa, 37 microalgal species, 24 holoplankton species, 22 meroplankton taxa, and 10 meiofauna groups were revealed, 24 species of microscopic mycelia fungi were attributed, and 28 morphologically distinct bacterial stains were isolated. Potentially toxic microalgal species were found: the dinoflagellates Dinophysis acuminate and Prorocentrum cordatum and the diatom Pseudo-nitzschia pungens. The tropical-subtropical copepod Pseudocalanus inopinus was recorded in ballast water. Polychaete larvae of the Polydora genus with an unusual morphology, which were not occurring in the Peter the Great Bay previously, were recorded as probable southern migrants from the coastal waters of the southwest coast of Honshu Island. Live larvae of the hermit crab Diogenes nitidimanus were revealed in ballast water, supporting the possibility of introduction of this species in the Peter the Great Bay. Based on an analysis of the total number of colony-forming units of heterotroph microorganisms (within the order of 103–104 cells/ml), the ballast water of ships sailing on the Russia-Japan line was characterized as moderately polluted. The detection of Escherichia coli strains, exceeding the standards quoted in the International Convention by three times or more, showed the potential danger of a mass bioinvasion. Conditionally pathogenic and toxinogenic mycelial fungi, which are able to induce mycoses and mycotoxicoses in invertebrates and fishes, were isolated from ballast water. It was determined that ballast water of the “rusty” type was poorly suited for the existence of zoo- and phytoplankton forms. In the case of the construction of an oil terminal in the Peter the Great Bay, a sharp increase of the introduction of exotic species via the ballast water and foulings of tankers is inevitable