Since I have had to sit through the various nasty details of how sewage treatment plants work in marine pollution classes and in various meetings on water quality in Narragansett Bay I thought I'd share something about how this works.
When one of these overflows happens it is because the water is flowing in faster than they can treat it and they don't have adequate capacity to store the excess until they can catch up. This will often happen after a big rain event even if the plant doesn't malfunction just because it doesn't have the capacity to handle it. The Fields Point plant in Providence has had huge problems with this, and pretty much overflows after any major rains event. It is currently being upgraded to reduce these incidents.
When an overflow happens they usually still do the "primary" treatment step to remove solids so you should not see any "harbor trout". If you see that kind of thing it probably came from a boat illegally dumping its head. What the plants are skipping in an overflow is "secondary", and "tertiary" treatment steps (most US treatment plants don't do full tertiary treatment) which take more time . These steps include disinfection and the removal of various dissolved contaminants. The main danger of these overflows is all of the pathogens that get dumped into the water because disinfection was skipped.
If anyone wants to know how this process actually works, this is a really good summary:
http://en.wikipedia.org/wiki/Sewage_treatment
