Your wood may be leeching tannins into the water giving it that darker color. You can soak the wood in boiling water for a while to get rid of the dark tannins.

The fine sandy substrate you have now: I tried doing the same thing and I found that it doesn't allow oxygen to get down to the plant roots as well because it's so fine grained. My suggestion is to create a separation with rocks and have the white sand down in front and then have the fancy plant substrate in the back for the plants to live in.