Hundreds of dead fish were spotted floating by the banks in places like Riverside Park and Edgewater, New Jersey.
Officials say they are bunker fish, or Atlantic menhaden, which are a kind of herring found in the Hudson.
The cause of death is under investigation, but it is likely that rising water temperatures deprived them of necessary oxygen.
Fish such as bunker that swim in large schools are particularly vulnerable to low dissolved oxygen content, the New York State Department of Environmental Conservation said.
Health officials say there is no cause for alarm.
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