The discoveries of the needles forced lifeguards to urge beach-goers not the enter certain areas of the water.
After days of storms, the syringes were found on several beaches, such as Monmouth Beach, Sandy Hook and Long Branch, according to WNBC.
The syringes were found after sewage systems in New York and northern New Jersey, as well as New York harbour, released sewage during the heavy rains.
The most likely explanation is that the syringes come from diabetics who flushed their needles down the toilet after use, beach patrollers said.
With dozens of syringes being found on Monmouth Beach just on Sunday, patrollers warned visitors that there was a significant risk of stepping on the needles if they ventured into the water.
Workers at Seven Presidents Park have said that more than 100 needles have been recovered so far.
Beach officials told WNBC that patrols will continue below the high tide line. They expected some closures and warnings to continue throughout Monday.
Following Hurricane Elsa, parts of New York City was flooded, with social media videos going viral of people wading through flooded subway stations as the water came cascading down the stairs.
The service said there’s “potential for heavy rain and flash flooding across parts of the northeast tonight and especially Monday and Monday night, particularly [in] poor drainage areas in the NYC metro region”.