The biodegradation of hydrocarbons by microorganisms is one of the primary ways by which an oil spill is eliminated from contaminated sites. One such spill was that of the Russian tanker the Nakhodka that spilled heavy oil into the Sea of Japan on January 2, 1997. This paper describes the three main processes of the Nakhodka oil spill, including: (1) the weathering of hydrocarbon-degrading bacteria (genus Pseudomonas) and crystallized organic compounds from the Nakhodka oil spill-polluted seashores after nine years; (2) the laboratory-scale biodegradation of the Nakhodka oil spill over a 429-day period; and (3) the bioavailability of kaolinite clay minerals and the role they play in seawater polluted with the Nakhodka oil spill.Upon the slow evaporation of the Nakhodka oil spill during the 9-year weathering, the dendritic crystal growth of paraffin (a mixture of alkanes) occurred in the oil crust under natural conditions. Heavy metals were obtained in the original heavy oil samples of three seashores in the Sea of Japan. Si, S, Ti, Cr, Ni, Cu, and Zn were found in the original Nakhodka oil spill samples whereas these heavy metals and S were no longer present after 9 years. The anaerobic reverse side of the oil crust contained numerous coccus-type bacteria associated with halite. The hydrocarbon-degrading bacteria and paraffin wax in the oil crust may have a significant effect on the weathering processes of the Nakhodka oil spill during the 9-year bioremediation.A biodegradation process of heavy oil from the Nakhodka oil spill by indigenous microbial consortia was monitored over 429 days in the laboratory. The indigenous microbial consortia consisted of bacteria and fungi as well as the bacterium Pseudomonas aeruginosa isolated from Atake seashore, Ishikawa Prefecture, Japan. Both bacteria and fungi had a significant role in the observed biodegradation of heavy oil during the 429-day bioremediation with respect to the pH of the solution. Hydrocarbon-degrading bacteria had a tendency to play the greatest role under neutral to alkaline condition (pH; 7–7.8). On the contrary, when pH shifted to acidic (pH; 2–4) levels, the fungi took over to degrade heavy oil. During the period, the aliphatic hydrocarbons were reduced significantly but the aromatic hydrocarbons remained relatively constant even after 429 days of bioremediation.Experimental study was undertaken to investigate the bioavailability of kaolinite clay minerals and the role they play in seawater polluted with the Nakhodka oil spill. TEM/EDS imaging suggested that the clays present in oil-polluted seawater were capable of stimulating oil-degrading bacteria probably because Si from clays facilitates bacterial usage of oil and C-O-Na-Si complexes on the surfaces of bacterial cell walls are a stimulator for oil-degrading bacterial growth in seawater contaminated with the Nakhodka oil spill.