The man, 38-year-old Christopher Angulo, reportedly paddled out to the Jet Star coaster in a canoe in order to plant a flag atop the wreckage.
Angulo, a local, said he missed the pier and wanted to restore something that he was lost, ABC reported.
Charges are pending and will likely include trespassing, according to ABC.
The roller coaster, which looked like a scene from a horror movie in the days following the Superstorm, made headlines when the mayor of Seaside Heights briefly proposed leaving it in the ocean as a tourist attraction.
But after an uproar ensued, the wreckage was slated for demolition and removal.