Southampton Town police said workers at the house called police after a suspicious man was found on Lopez's property on Aug. 8.
John M. Dubis, a 49-year-old who lives on Rhode Island, was reportedly living in the pool house for a week. Lopez, the mother to twins with singer Marc Anthony, was not present at the time.
According to police, she already had an Order of Protection against him. The history of the court order was not immediately clear.
Detectives arrested Dubis and he was charged with second-degree burglary, a felony, first-degree criminal contempt, a felony, fourth-degree stalking, a misdemeanor, and possession of burglar tools, also a misdemeanor.
Held overnight, he was arraigned the next day. He pleaded not guilty, police said. He is being held on $100,000 bail.
The court ordered an exam to determine if Dubis is fit to proceed, according to police.
Though police did not provide the address of the property, it was recently reported that Lopez purchased a Water Mill property for $9.995 million.
Lopez isn't the only celebrity to deal with stalkers at their Hamptons homes.
Just a week earlier, police in East Hampton found a longtime stalker of rapper Sean "Diddy" Combs — an old boyfriend of Lopez's — near his Northwest Woods house.
Quamine T. Taylor, who was first arrested at Diddy's house 12 years ago and then again last year, was picked up on a marijuana charge, and released. Police said the 31-year-old Queens man didn't technically violate the Order of Protection that is in place, to stay away from Combs' and his waterfront house.