That's pretty damn good.
I like the sewage exit idea a lot. Although I have a feeling that in general, up until like the 1800's period they would've just poured straight into the bay or moats as they would've been mostly for rain runoff. Sewage would've likely been collected into pits and then carted out. Or so I imagine. Part of the difficulty would be that the natural flow of the blocked river would be fighting redirection of water, trying to get water to flow against it's natural ways almost always leads to issues especially in an environment that looks as wet as that one does.
Also I would imagine the islands in the mouth of the bay would be extremely hazardous to shipping in general and would almost certainly cause daily accidents in a port as busy as this one looks to be.