The brown water is from Tannins, which is a natural extractive from wood.
When wood is submerged in water, these tannins will leak out.
Over time, the tannins will stop leaking out.
The only way to clear it is to do water changes, or add carbon to the filter.
You should of soaked/boiled the wood for a couple of weeks, yes, a couple of weeks, prior to adding the wood to the tank. This way you will be able to get as many tannins out as possible.
Luckily, tannins are not harmful to the fish, and the fish will most likely like the tannins.
-FHM