In saying that, I experienced one natural wonder that I hadn't seen anywhere else in the world before on a road trip in Japan, and that is the Naruto Whirlpools.
The body of water pictured below is the Naruto Strait, which is a channel of water that separates Honshu from the island of Shikoku. The strait is part of what connects the Pacific Ocean with the Seto Inland Sea, and as a result there are a great deal of tides and currents moving their way around. That's where this natural phenomenon comes from. When they are at their peak, the currents can create whirlpools of up to 20 meters in diameter, with the water current also moving around 20 kilometers an hour!
When we visited, we didn't see any whirlpools that were quite that large, but we definitely saw a lot of the currents moving around and creating decent sized whirlpools! It was pretty neat to see. You can see some of the currents creating those circular whirlpools in the below picture. We got our vantage point from the Naruto Bridge Observatory (called the Uzu-no-Michi Walkway). I would definitely recommend checking their website prior to visiting (you can find their website here!) as it outlines for you the best times of day to witness the whirlpools. If you come outside of the best times, you're going to see much smaller whirlpools - they're still neat, but if you're wanting the real effect I think it's definitely best to try and head there to coincide with the peak times for the day.
Admission to the Uzu-no-Michi Walkway is 500 yen for adults, 400 yen for Junior or senior high school students, and 250 yen for Elementary School students. Children under that age are free.
There's also the Naruto Kanko Kisen which is a sightseeing boat, which lets you get a bit closer to the action than the vantage point from the walkway! If you're interested in checking the whirlpools out with that option, you can see their website here for more information.
If you're passing through the area, it's an interesting place to stop and stretch your legs at - and a great opportunity to see a really different natural phenomenon if you time it right!