You blockade the exit points in the rivers. Of course, that means passing the forts TWICE, once on the way in and once on the way out, which is really sucky for your blockade ships.
Distant Blockade refers to controlling the forts in front of the cites. I'm not sure if controlling the forts is equivalent to having a successful Brown Water Blockade, or only assist, but probably the former.
IIRC there was some planning and testing of actually blockading from outside the forts, but I can't find any reference to that having actually having been implemented, and I wouldn't know how I would recognize if it were there, so I don't think it is.