I'm pretty sure that the Mississippi River Delta as well as the drainage from Mobile Bay has a lot to do with the water being brown over that way. If you look at that area on Google Earth you can see how large the delta system is, hence an awful lot of silt being flushed out into the Gulf and brown, yucko looking water. As for most of the areas from around Pensacola to Mexico Beach, there's really no silt to speak of draining into the Gulf by comparison.