My blood boiled when i heard it and in a very un-scientific manner i challenged statements by Save the Sound. and a presentation on Nitrogen. My apologies, because for 33 years i researched this and even spent some time setting up your lab for chlorophyll analysis in Stamford. So what can i say - levels of usable nitrogen remained low for all of the warm water season (above 50 F). This was Nitrogen as Nitrate and nitrite. The early spring "bloom" of algae was NOT repeated except in special cases in harbors and did not go out to the sound. The levels of plankton also remained low even when Oxygen levels were low. Studying the sediment, i found very interesting issues. The "muck" was extremely high in anaerobic bacteria and Iron and sulfides/sulfate. Very determined chemical oxygen scavengers. They are there because of years of untreated discharges from treatment plants.
The next issue is that all Nitrogen is food and the lack of the nitrogen in the water is creating a very clean, but lifeless Long Island Sound. The initial die-off (in large quantities) occurred after tropical storm Floyd, after which high quantities of Hydrogen Sulfide were detected in the Long Island Sound water as much as half a mile off the coast line.
The lack of recovery is possibly multi-faceted, but a lack of a healthy plankton population can not be ruled out. Plankton need nitrogen to grow and they provide food as a first step in the food chain.
While i have officially retired, the data was presented and not researched by anyone further, yet many other papers have been written talking of other causes, including phosphates, which is a distinct possibility since long Island Sound is neither fresh, nor completely Ocean salty . Facts and figures i can not provide, but if you want to really look at the causes, look everywhere not just what you are told.