My boyfriend told me never to live on the east side of Tokyo because - as you say - it's below sea level and prone to flooding. I've always lived on the west side since i came here. You may have noticed that around the interior of the yamanote line, there are a lot more random slopes as you walk around and the land's not so flat-- Yamanote actually means the "mountain" side of the city, as opposed to Shitamachi or "down-town" on the east side around the sky tree, asakusa, shinbashi, etc, where you saw all the rivers.