These are canals that sit within the subdivisions along the shore. Most of the people use it to tie up their boats and some like it because it is green mucky water but serves no other purpose but as a place for Fish Flies to hang out before becoming road kill.
I heard they were man made, or most of them were but they have retaining walls and docks.
Most of what you are calling "canals", if I got what you are speaking of, were either channels through the marshes that were once in the area and then were dug out when the marshes were drained or there were a few dug for the reason you suggest.
From what little I know of the PCB pollution the sources have long since gone. What is happening now is when they dig it up it stirs up the muck and releases trapped toxins back into the water. They were able to clean up the "Black Hole" near Humbug Marsh a few years ago They used a "vacuum" system to extract the mud and did very little "digging" They took out muck down to almost 15' IF I remember correctly. It is been a very long time since I talked to anyone on this subject.
My first move, if I had control, was to consult with people who know far more than I do on the subject. The Corps being one. Chemical people etc. I would like to see 2 or three serious plans, cost vs. benefit etc.
I would be in favor of sealing them off, short term. The last I talked to someone on this the line of thinking was that as slit covers the bottom it will "seal" the PCB's in place and they will more or less stay there unless disturbed. Maybe a combination of sealing, using a vacuum like they did at Humbug would work. I would need to consult with experts. I would be hiring the best I could find. As governor it is NOT my job to know all the answers. The governor is a manager. A good manager sets the goals, hire the best he/she/it can find to meet those goals, and let's them work.
As to the fish flies, they are a clean water species that require high oxygen levels in the water. They were in bad shape and in heavy decline in the late '60's through early '70's as local oxygen contents were falling everywhere. As the water has been cleaned up they are coming back nicely. Good thing too. They are a major part of the area's life cycle.