**Edit 2:**
This does still work, but you will have to log out after placing the solid blocks. When you log back in the game will not have remembered there was water there. This has only been tested in single player.

**Edit**:  
The following no longer works as of 1.1.

**LEGACY ANSWER**:  
If you place a block on an area covered with water, the water in that spot will be destroyed. You can eliminate the water by simply filling the pool with dirt or stone squares (you don't *need* sand) and then mining them back out again.