There are surely many examples of these in Tokyo: houses or other buildings that were built along a river, stream, or canal. The waterways were subsequently filled-in, but the properties remain.
Here is an especially interesting example, in Edogawa (Google maps).
First, a map. The building is indicated with a grey dot, at the confluence of two streams.
Here’s a picture of the house, facing north:
And a view from the house, facing south: