From an economics perspective, I would expect to see larger facilities close to the river (possibly even closing it over in its upper reaches) as well as having piers built out into the river to get the cleaner, less contaminated stuff. There should also be a major road heading directly to the fortress (or possibly a slide for meat chunks down the major sales yard in the city). I understand the desire to have a cleared area around the fortress, but I would also expect that folks would want to get as close to the source of their desire as possible; maybe a city wall-style element built from the side walls of the closest buildings?