The Peconic Estuary offers extensive recreational access with multiple paddling trails including the 9. 5-mile Peconic River Blueway and the 5-mile Coecles Harbor Marine Water Trail, plus numerous kayak and canoe rental facilities throughout the region.

Multiple public launch sites are available at state parks and county facilities, with several offering boat rentals, fishing access, and seasonal amenities like parking and restrooms.

The estuary supports diverse recreational fishing opportunities across freshwater ponds and saltwater bays, with designated fishing sites at parks like Montauk County Park, Cedar Point, and Indian Island County Park.