Yep, the wood is turning your water brown. It's caused by the leaching of tannins from the wood into the water. It will go away with time but will depend on what type of wood and how large the pieces are. Someone else will have to help you with that, since I don't know how long leaching normally occurs for. I don't think it would be harmful to your fish, unless it's in excess amounts. Keep doing water partial water changes weekly, and you shouldn't have any problems.
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