My place is up that way, and I asked around about this phenomenon before I bought it . It was explained that the effect was from tannins leaching into the water from leaves, coupled with the lack of mixing with fresh water as mentioned earlier.
http://en.wikipedia.org/wiki/Tannin
In the "brown wake" areas, the bottom of the lake will be seen to have rotting leaves/muck on it, while the "green wake" areas will be seen (generally) to have a rocky bottom.