Character called The Prime controls water [s]

[Donna]

a different world, the main character was female and her father removed her from her family but then he died and she lived by the river in a tent then she discovered who she was. She then took her place with her family and was known as "The Prime"

[Michelle Mulford]

Troubled Waters. If you haven't read anything else of Sharon Shinn's, you should really try her Angel series, starting with Archangel. I also enjoyed her Mystic series, beginning with Mystic and Rider.

[Joseph]

Michelle is definately correct, that's "Troubled Waters." I'd also suggest if you like the elements theme of this work of Shinn's, check out Mercedes Lackey's retellings of fairy tales with elemental wizards, the first is The Fire Rose.

[Lobstergirl, au gratin]

Donna shelved "Troubled Waters" in February 2012 so I think we can call this one solved. Unless she was just shelving it because it sounded interesting....