The widespread deaths of Atlantic menhaden, and possibly other species, are most likely the result of prolonged heat and lack of rain, combined with other factors, which reduce levels of dissolved oxygen that the fish need to survive.
Low oxygen (hypoxia) or no oxygen (anoxia) can also occur in water bodies when excess organic materials, such as large algal blooms, are decomposed by microorganisms. During this decomposition process, oxygen in the water is consumed.
Sewage pollution and fertilizer act as “nutrients” that fertilize phytoplankton and spur algae growth. Scientists have determined that the Hudson is the most “nutrient rich” estuary on earth.
So the river starts from a compromised position, with over-nutrification from sewage and fertilizer.”
“When millions of menhaden swim into the estuary and consume the limited oxygen, ‘they will suffocate themselves,’”
Bob Walters of Yonkers, who retired last year as director of the Yonkers Science Barge, has seen the phenomenon before. “This is an extraordinarily large die-off,” Walters said. “It doesn’t happen every year, but it happens.”
But, Walters said, it’s not so easy to ascribe the die-off to a sign of a declining Hudson. “The river’s a complex system.”
Later this summer, when we get a series of rainstorms or cloudy days, we’ll see lower water temperatures and less algae growth, and we’re likely to see a reduction of fish mortality as oxygen returns to adequate levels.
But we should consider this yet another warning that we need to restore the baseline health of the Hudson and New York Harbor in the face of climate change and ever-increasing global water temperatures.
Text source, from the articles: “Dead fish along the Hudson River: Why it’s happening and what it means” by Riverkeeper published on July 2nd, and “Thousands of dead fish found floating in the Hudson River. Here’s why” by Nancy Cutler published by lohud on July 6th, updated as of July 7th. Much appreciation goes out to Riverkeeper & Nancy Cutler!
The photos and videos, however, are provided by me, and not affiliated with lohud or Riverkeeper. Captured Monday evening, July 6th at Riverside Park
Jonas St. Juste 
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