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Summary: Algae should be scrubbed off of a turtle's shell so that it doesn't stay permanently attached. Clean turtle shells of green algae and scutes with tips from a reptile specialist in this free video on turtle care.
"Hi, I'm James Dix from Reptile Rescue Service in Salt Lake City, Utah. In this episode we're covering how to clean an aquatic turtle, such as a red-eared sliders shell, when they get dirty. A lot of times the tanks, when people don't keep 'em clean enough, they get an algae build up on 'em. And it comes off pretty easy. Just use a common household scrub brush for your dishes. Reach down, grab your turtle out of the water. And you don't want to push super, super hard, but just kind of go in a circular motion, and you'll actually see the green algae peeling off. Breaking off. Dip 'em in the water, and go over it a few times, and it'll come off real easy. When you see the build-up, you want to make sure you get it off as soon as possible, because the longer it stays on the harder it is to scrub it off. Sometimes it stays on permanently if you leave it too long. The shell, actually as the turtle grows, the scutes will break off, and the algae will come off with those at the same time. So if your turtle starts to peel, it looks like, this is normal. This is not a disease, or anything. On a desert tortoise, if you have a lot of 'em where they're digging, get a lot of dirt, and a lot of times in captivity, if they're not outside where they would be digging, they get feces build-up on 'em. You would just flip 'em over, hold 'em upright. Don't lay 'em completely on their back. Take a hose, get 'em wet, and start scrubbing down in the grain of the shell, and it will come off. Never lay a turtle or tortoise on it's back, because it can suffocate from this."
eHow Article: How to Clean Turtle Shells