Join Date: Oct 2015
Location: Guelph, Ontario, Canada
Turtles are pretty dirty animals, they make far more waste than any fish in my experience. It's good that you bought a canister filter right away, that is something that I put off for far too long.
As WaterLife said, the filter will take some time to properly colonize with good bacteria that will help clean the water. You can help speed this up by adding Tetra SafeStart. Until then, change the water often, and lots of it (I would suggest 1/3 of the tank every week until it stabilizes). Add a dechlorination liquid to the new water or else the chlorine in the tap water that keeps your drinking water safe will kill the good bacteria that you are trying to grow in your tank.
As well, a coarse gravel on the bottom of your tank might help. I had very fine sand for a long time, but my turtle swimming would stir it up and make the water very cloudy. Coarse gravel will catch more waste materials, but then you have to be sure to vacuum it out (but gently) when you change the water.
Last thing: try to be very careful about not feeding your turtle too much. Excess food is the easiest way to pollute the water. I have almost always had a few fish in the tank with the turtle: they help keep him entertained, and also eat up some of the fine crumbs that your turtle might miss. You can get something like white cloud minnows easily from most pet stores, and because they are very inexpensive it won't matter as much if the turtle catches one once in a while.
Hope that helps!