The nitrogen as nitrate and ammonium acts a fertilzer causing large algae blooms in the spring During the summer the algae die, sink to the bottom and accumulate. The bottom water in the sound is cooler, thus more dense and does not interact with the overlying warm water.
Bacteria eat the dead algae consuming oxygen in the process.
This depletes the bottom water in oxygen leading to hypoxia. Hudson River Headwaters are in the Adirondacks. The river is 315 miles long. An estuary up to Troy. From Troy to NY, the difference in level is 2 feet.