Several thru-hike trails have water-sections. For example, the American discovery trail requires crossing the Chesapeake Bay under the bay bridge (no pedestrians allowed). This is a 6km stretch of water that drops to 5C in winter. There is no? public transport across the bridge. Be wary of water currents in any body of water.
But how would self-supported group of thru-hikers cross it? A self-supported thru-hike is extremally difficult. Do not attempt without extensive training, preparation and emergency rescue measures.. That being said, for a self-supported trip you will have to carry all your non-disposable equipment for the entire duration so weight restrictions are severe.
Inflatable kayak/canoe. Weights far less than any rigid hulled boat.
In-situ construction: Make a single-use canoe out of reeds and other available materials. Probably a very dangerous and time-consuming way to spend your zero-mile day. Maybe just for the paddles.
Wet-suits (or even dry-suits). Seal your gear in a bag with a trapped air-bubble for buoyancy.
A multi-use strategy
Ideally, the equipment used for crossing water is not dead-weight for the terra-firma majority of your trip. A wetsuit could double as an extra layer in very cold weather. A deflated inflatable kayak may also be used as a water-proof barrier for camping in wet areas.
What is the general aquatic strategy for a mostly land-based trek?