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For Nagas specifically, they also have the Water Spring building that will (like the fountains in the Clear Threat mode) spread water around it.

Also, I think Lunord has a spell to create water, but the Nagas aren't big on religion.
 
"Lower the lands" if used on plains will create water.
Note that the single hex version Lower the Land (note the missing s) will not let you sink land.

The Lunord spell is Lunar Tide which requires 25 points towards Lunord and is a Tier 3 research. It will turn any tile inside the area into a water tile, unless there's a structure on it.
 
Also note that certain Naga buildings (such as the Harpy and Gorgon buildings) require land, so you can't just turn everything to water. That's what separates you from those bad nagas who drown even their gorgon "allies". =)