In my first session of our gestalt game I used this spell to considerable effect.
First off, I wasn't a PC. I arrived unannounced to my home group's session (I am at college, 2 1/2 hours away from home) during a weekend when I happened to be home. As all of you know gestalt characters take a while to create. They were 5th lvl, which isn't a lot of work but it would've killed the session to stop and make a character for me.
So instead the GM put me in charge of the NPCs. Another player in my exact same circumstance also played an NPC, but she was one of my lackeys. My character was a Yuan-ti abomination cleric, worshipped as a god by a tribe of lizardfolk that had come up against the PCs.
The PCs were in a swamp, camped out, defending against guerilla tactics from the lizardfolk tribe. The lizardfolk were losing.
My first move was to plan a routine strike, but remove the PC's advantages. So I stayed REALLY far away (Whatever the range of Control Water and a tree-controlling spell I used allowed) so that they couldn't get line of sight on me (They had an archer who could shoot out to a mile and do damage like a machine gun).
I sent archers in to surround the PCs at a distance. These archers were led by the other player who didn't have a gestalt character. I don't remember the name of the spell I used first, but it allowed me to move trees to some extent. So I slither up a tree, at an incredible distance from the PCs, cast the spell that opens the trees up in a line to the PCs in order to gain line-of-sight on them, cast control water, and then the trees would close back up so no one could fire back at me. I used the "raise water" part, and brought the waters of the swamp up around them. My lizardfolk archers moved in and shot every PC who swam to the surface or out the sides.
We scored no kills, but the water eventually fell and splashed out into the swamp, completely wrecking their camp and losing most of their gear (Which still mattered to some of them at that level).
The PCs could not gain a good night of rest due to lack of a suitable camp and gear nor could they let their guard down because I kept scouts watching them.
My next move was a magnification of the previous tactic. The water itself was a great battlefield controller but my NPC offense was still limited. So I next sent scouts out in several directions.
One group went to the camp of nearby giants (I don't remember if they were hill or stone giants) and, using a fireball that I had provided for them via item creation, fireballed the nursery. They then taunted the giants so that the giants would give chase. Of course I made sure my lizardfolk scouts looked liked the PCs first.
Another group went to an area of the swamp where we knew some prehistoric crocodiles (I believe they were called megalodons?) resided, and started chumming the water in between the megalodons and the PCs. "Chumming" is where you throw bloody meat into the water in order to attract predatory aquatic creatures.
Yet another group went to a nearby cave to draw out the local hydra. They managed it, but the hydra mostly failed to matter.
The giants arrived at the PC camp first and engaged the PCs. As soon as that happened I executed the same spell combination (Open trees from a distance, cast control water, close trees) and soon after the megalodons showed up. In the water the PCs had to deal with giant crocodiles and giants (The giants were as hindered by the water as the PCs), outside the water they had to deal with lizardfolk archers and giants.
Two PCs almost drowned, a couple others weren't handling the constant assault well, and one of them ended up calling in a favor from a god to get the part out. That favor cost him, although not near as much as I would have liked, it did cost him.
I was planning another similar assault when the session ended. At that point the PCs were running out of everything that required rest to recover, and they were starting to take penalties for not sleeping. I didn't return the following week (Or for a few sessions, due to school) but it's my understanding that they retreated from the swamp, which was all the lizardfolk had ever wanted anyway.
The spell has its uses. Now all of the things I did aren't necessarily within the realm of PC ability (I was 9 or 10 levels into cleric, the GM didn't give me a character sheet so I just used spells mostly), but if there is water around control water is a pretty decent BFC spell. Even if an enemy has a swim speed they have to decide whether to fight in or out of water and just being in water is a pretty severe hindrance. In a naval campaign it could be fun to bury the enemy ship in water (It'll move just about everything on the ship from useful to useless and screw up the crew) or if you're just in a swamp a lot of stuff isn't actually aquatically optimized.