same thing used to happen to me. What your doing is displacing all the beneficial bacteria. You need to retain that bacteria somehow, or replace it by using products like Cycle, or Waste Control. Almost any fish store out there sells that stuff.
If your filter has chambers to hold stuff use ceramic rings or biomax.. using those allows you to house bacteria cultures which are necessary for the breakdown of waste your messy turtle will generate. Get some rings if you can. And don't clean them. Keep them real dirty.. to the point where they're almost oozing..

Well.. you can rinse them off every half a year or so if you like.
But that should take care of the bacteria bloom your experiencing.