During World War II: The Imperial Japanese Navy used the harbor and port as a submarine base. Wakkanai was far enough north to be outside the range of American heavy bombers and was safe from air attack. Until the early to mid-1960s, the northern portion of the harbor remained divided by concrete sub-mooring pens. The large breakwater structure was actually a sub-repair facility. At the shore end there was a huge winching mechanism capable of hauling subs up into the partially enclosed structure where they could be repaired while completely out of the water. Built into the hills above the city there were several reinforced concrete bunker-type caves where they were used either to store ammunition and armament, or as air raid shelters for the civilian populace. History would suggest the former use, rather than the latter. During a re-build/renovation of the harbor sometime during the 1960s or 1970s, the harbor was cleared of the concrete pens and the machinery was removed from the breakwater structure which was reconfigured.
Geography
Japan's northernmost point, Cape Sōya is located in Wakkanai, which is on a peninsula jutting towards Sakhalin Island in Russia, which it is 43 kilometres away from; on a clear day, the Russian island can be easily seen. There is also Benten-jima located northwest of Cape Sōya.
Wakkanai has a humid continental climate typical of Hokkaido but with strong influence of the ocean as island portions near the great land masses, with cold winters, warm summers and generally heavy precipitation from the Aleutian Low, whose winds hit the city direct from the Sea of Japan but with strong oceanic influence. The winter is cold enough not to fall in a "Cfb" climate and the summers although very mild for typical climate "b" is warm enough to fall into a "Dfc", both in the classification of Koppen. The mean annual temperature, at, is the second lowest for a significant population centre in Japan after Nemuro. Snowfall at, the third highest for a big city in Japan after Asahikawa and Aomori and one of the highest anywhere in the world. For comparison, Nain in Canada receives of snow. The Aleutian Low also makes the sunshine hours the lowest of Japan's major population centres and in the winter the wind speeds are the highest in Japan with an average of, which adds to the cold of a typical winter day. The city's port is usually usable throughout the year, but does occasionally freeze in cold winters.
operates seasonal ferry service to Rebun Island and Rishiri Island. Ferry service to Korsakov on Sakhalin Island was terminated on September 18, 2015. Wakkanai governor KUDO Hiroshi pledged to restore ferry service to Sakhalin and in 2016, the route resumed operation between the months of June and September of each year and is commercially operated by the Commonwealth of Dominica flagged vessel Penguin 33, which is a High-speed craft owned by and operated by .
