When the location for the new capital was being scouted in the 700s, court geomancers remarked that the city was well protected in the northwest by Atagosan and in the northeast by Hieizan two mountains that tower over the city today. The mountains are part of several groups of mountains, Higashiyama, Nishiyama and Kitayama, that surround the city on three side creating the Yamashiro Basin which is listed by Wikipedia as having an average elevation of around 1,000 meters. But that is a bit misleading. A good portion of the city itself is at an average elevation of around 86 meters forming a basin known as a 'bonchi.'

Here is a very good map with certain points marked by elevation. My apartment is directly across the street from number 1 on this map.
Two major rivers run through the city and feed into the Yodo River which flows on to Osaka and into Osaka Bay which opens onto the Inland Sea and the Pacific Ocean.



If you are unfamiliar with the area, please note that the large body of water you sea directly to the east of Kyoto (although not on these maps) is Biwako, the largest lake in Japan. It is not connected to the sea.
Now, all of this is not to say that there is no worry of earthquakes in Kyoto. There are fault lines in the city. But that applies to anywhere in Japan. We also have a lot of green space, a large aquifer, no high rise buildings (not that high rises are dangerous and smaller ones are safe necessarily) and many broad streets.
One further note for those not familiar with Japanese geography.

Thank you for your concern and I hope this makes you feel better.
(if there are any mistakes in my data, please let me know. there were lots of conflicting average elevations)
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