The Sheriff's Office maintains a Marine Patrol Unit that patrols two bodies of water during the summer boating season. The Allegany Reservoir, which is the site of the county-owned Onoville Marina, is a very popular summer recreation area. This lake borders the Allegany State Park, Allegany Indian Reservation, and crosses over the state line into Pennsylvania. The second body of water, Lime Lake in the Town of Machias, is a small lake that is very popular and is extremely busy with all sorts of water related activities.

Deputies assigned on Marine Patrol are certified for Marine patrol with their duties being to conduct safety inspections, enforce New York State navigation laws, assist stranded boaters, and investigate boating accidents. They also assist with search activities and rescue operations as needed.

The Marine Patrol Unit is partially funded by New York State which helps offset the costs to the Sheriff's Office.