it's sad, but by the time it reaches the bay hardly out of the ordinary unfortunately.
happens pretty much any time it rains hard with all the combined sewer/storm water systems discharging directly to the waterways. it's why down the shore after a good rain the coliform counts go up.
take a look at the map of all the NJ CSOs dumping turds... about 95% of them end up in raritan bay
http://arcg.is/1DBBruT