The Port Jefferson Harbor Complex is just that — a complex cluster of waterways that needs diligent eyes watching over it.

Those eyes belong to Brookhaven Town Harbormaster Peter Koutrakos and the others in his department, who are all working to keep the water safe this boating season.

The harbor complex includes Port Jefferson Harbor at its center, where Koutrakos is based, as well as Setauket Harbor and the adjacent Little Bay; Pirate’s Cove; Conscience Bay and the Narrows that lead into it; and a small section of water immediately outside Port Jefferson Harbor on the Long Island Sound that is bookended by Old Field Point to the west and Belle Terre’s Mount Misery to the east. Between these sections, the complex has more than 2,000 acres of surface water, and that area sees thousands of boats every season.

Peter O’Leary, the town’s commissioner of public safety, said between moorings and slips in the area, there are more than 1,200 spaces for boats, and that doesn’t include the ones just passing through.

On any given summer weekend, “the place is bedlam,” O’Leary said. “It creates quite a bit of traffic.”

With heavy traffic comes risk.

For Koutrakos, who has been harbormaster for 14 years and has jurisdiction in all town waters, it was the attack on the USS Cole in 2000 — an al-Qaida suicide attack in Yemen in which a small vessel next to the U.S. Navy ship was blown up, killing 17 Americans — that made him realize boats could be used as weapons.

Things also changed after the 9/11 terrorist attack. Officials became aware of the harbor’s vulnerability, as possible targets for terrorists include power plants, oil terminals and ferries — and Port Jefferson Harbor has all of them. Long Island has also been a concern in national security discussions because it is close to New York City and at the same time is remote: Ferries would be the only way off the island if an emergency event were to shut down transportation into the city.

To keep the complex safe, the harbormaster works on a number of security exercises. One program, Operation Shield, involves coordinating with other agencies to randomly check foreign vessels for travel documents.

Though Operation Shield only runs on certain days, Koutrakos said he regularly does checks on his own. If the vessels do not have the proper documentation, he calls in customs officers to board and search them.

Another exercise he occasionally works on is search and rescue training with the U.S. Coast Guard, which helps prepare for an emergency situation, for instance if the ferry were to sink due to a mechanical problem or a bomb.

Koutrakos explained that the exercise group determines how to respond to an incident and who would take command of the scene. In the case of the ferry, officers also talk to the captain to learn how he would respond under certain circumstances and discuss a strategy for saving as many lives as possible, “before something really happens.”

The harbormaster also meets every few months with a Long Island security committee whose members range from the local to the federal level.

To boost security all over, O’Leary said, the town is working to install security cameras on its properties, and Port Jefferson is slated to receive some of that surveillance.

However, one of O’Leary’s concerns in protecting town waters is linked to the economy. He said budget cuts have meant cutbacks on seasonal employees, so there are fewer bay constables on both shores and they are working a shorter season. There are also fewer workers to pump out waste from the boats so it is not discharged into the water.

On Koutrakos’ end, he has an assistant harbormaster year-round and two seasonal harbormasters during the summer.

Most summer days, Koutrakos spends his time patrolling the waters and helping people who call him for assistance.

‘The place is bedlam. … It creates quite a bit of traffic.’
— Peter O’Leary

Born and raised in Port Jefferson, Koutrakos has a name people might recognize — his family owned the Elk Hotel and Restaurant on Main Street before it went out of business. He wife, Carol, works for the Port Jefferson ferry.

He has been around long enough to see security at the harbor change over the years. Before 9/11, if someone were to leave a bag at the ferry terminal, an employee would grab it and ask if anyone had left it behind. Now there are security protocols in place to handle such a situation. Before, there weren’t any restrictions on taking photos or video of the harbor. Now officials keep an eye out for people capturing the ferry terminal or other sensitive areas.

One thing that hasn’t changed is Koutrakos’ “only gripe with the job” — he isn’t permitted to carry a sidearm while he is on duty, though he is licensed to carry.

Other marine law enforcement agents carry a sidearm, including those from the Coast Guard, the Suffolk County Police Department’s Marine Bureau and the state Department of Environmental Conservation.

The harbormaster said he never knows what situation he will find himself in and “should we get put into a lethal force situation, the fact of the matter is we have no way of defending ourselves or the public.”

Despite this sticking point, another thing that hasn’t changed is Koutrakos’ playful personality and his passion for all things marine.

He has said he enjoys his job because he gets to be on the water and he gets to help people: “At the end of the day, tired or not, it makes you feel better.”