The Nakhodka, a Russian tanker loaded with 19,000 kL of C-type heavy oil, was broken up into sections and submerged off Oki Island, Shimane Prefecture, Japan on 2 January 1997. The bow, after drifting for four days, was wrecked off Anto, Sakai City (Mikuni), Fukui Prefecture, threatening the environment throughout the various shores of Ishikawa Prefecture. The accident, caused by a heavy oil spill of 6200 kL, created serious environmental problems along the shores of Hokuriku District. We report the characterization of C-type heavy oil 20 years after the accident at the Atake seashore, Wajima City, Ishikawa Prefecture, in the Sea of Japan, based on observations in the field on 18 January 2017. We studied the microstructure, mineralogy, chemical composition, and radioactivity associated with microorganisms in the soils, and buried fishing nets and ropes that were contaminated with C-type heavy oil from this spill. The analyses used a combination of micro techniques, analytical data based on a CHN analyzer, X-ray powder diffraction (XRD), and two kinds of scanning electron microscopy equipped with energy dispersive spectroscopy (SEM-EDS). Hydrocarbon-degrading bacteria, paraffin wax, cristobalite, graphite, calcite, halite, and biotite from the Nakhodka oil spill were recognized on the surface of ropes and in the soil of the polluted seashores after 20 years. The chemical compositions indicated that high concentrations of C, O, Na, Al, Si, P, S, Ca, Fe, Cl, Sr, and Pb were predominantly indigenous to the Nakhodka oil spill. In the XRD analysis of the oil-contaminated soils on the rope at the Atake seashore indicated paraffin wax, graphite, sulfate, calcite and halite refractions with clay minerals, after 20 years. To date, no report has described the results of electron microscopy observations, such as Micrococcus bacillus and filamentous fungi, found in oil-contaminated soils after 20 years. In this research, such observations are introduced as “bioremediation” by hydrocarbon-degrading bacteria, graphite, and paraffin wax. On 18 January 2017, the reflection of graphite, paraffin wax, sulfur, calcite, and halite with clay minerals confirmed the occurrence of bioremediation. Many kinds of hydrocarbon-degrading microorganisms—such as filamentous fungi—were found in oil-contaminated soils after 20 years. We have used SEM-EDS to show semi-permanent bioremediation and biomineralization processes after 20 years.