with every piece of terrain under a certain height automatically "inflicted" with it.
i have to disagree here... although i need to speak to hyronymus about this...
i suggest that when creating a map (not sure how to do this using random maps), the land is created in its entirety, and you take the bucket of water tool, and pour water into an area. you decide how high the water goes and you can change it while previewing the map. you also have a tool that creates an area where water is generated and runs downhill (ie, marshland that supplies rivers)
and then you have aquifers. water doesnt automatically appear if you lower land below sea level. it appears if you lower it into a water basin (aquifer), this can be above or below sea level. although near the sea, it would be at sea level and would cover a large area adjacent to the sea.
anyway, the benefits of having water as "inflictable":
water depth to control ship movement (you cant have a giant container ship going up a small stream)
perhaps some submarines (more discussion on this later)
land below sea level
tunnels under seabed
tunnels on sea bed
tunnels suspended from sea bed
tunnels below sea level (on land)
perhaps some more that i just cant think of
to the best of my knowledge, these are impossible when using water as a terrain type