Crews desperately tried to rescue the man after the accident on Tremley Point Road in Linden around 8 a.m., but their efforts proved unsuccessful.
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Police said the excavator got too close to the water and toppled over into about 6 feet of water in Arthur Kill, estimated to be approximately 40 degrees.
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It took rescuers and divers an hour to reach the victim.
"Ultimately, the victim was taken out of the crane by NYPD Aviation dive team, along with the Linden Fire Department, rescuers and a Zodiac boat that we had deployed into the water," Fire Chief William Hasko said.
He was rushed unresponsive the hospital, where he was pronounced deceased.
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"The individual was ultimately removed from the cab and transported to Trinitas Hospital," Linden police Lt. Chris Guenther said. "OSHA will be the lead investigative agency on this."
The investigation is ongoing, and it is unclear if wind was a factor or if the vehicle was just too close to the water.
The company involved, Simpson and Brown, did not have a comment on the incident. According to their OSHA record, they do have an open investigation from an incident in August.
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