How can I /fill water?

Solution 1:

Try /fill ~-80 69 ~-80 ~80 69 ~80 minecraft:flowing_water.

Solution 2:

I had a similar problem, so I wrote a mod to do it (and other things) for me.

Grab a copy of the Builder's Helper mod from http://www.minecraftforge.net/forum/index.php/topic,26612.0.html . This needs Forge and minecraft 1.7.10 or 1.8.

This comes with a 'blueprint' called 'water-table'. Give yourself the builder's wand item, use /wand set water-table, then right-click the wand in front of the hole you want to fill. It will fill up with water to the level you clicked. It will not remove any existing blocks from the world.

There is a similar plan to evaporate existing water, plans to build houses, glass dones, and so on, as well as copy existing structures.