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A lot of people just siphon it out and replace it periodically. Petco has a $20 submersible filter pump that contains a carbon cartidge. If you have room to put that somewhere in there, it might keep the water clearer longer.

Is there anywhere else that something other than gravel is touching the water like a log, or some leaves?

I wouldn't worry too much about it though. That tea colored water is more of an asthetic thing than any, it doesn't harm to the frogs.
 
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