Paddle and Pedal Shuttle Solution
Floating down a river is one of the great pleasures of life. Getting back up the river is one of the great tricks of canoeing, the Raison d'être for a lot of canoeing clubs.
Almost all rivers have a descent way back on a bike...some are truly spectacular, like the Paulinskill Valley Rail Trail which parallels the Paulinskill River in Sussex county and Old Mine Road which runs along the NJ side of the Delaware River. But since both rivers and roads follow the path of least resistance, roads usually follow rivers.
Biking back often gives you a different view of the corridor you just paddled thru--not as slow as walking, not sequestered from the terrain like in a car and since you are the motor, very sensitive to the nuances of the terrain.
Most folks lock the bike at the pull out, drive to the put in, paddle down and ride back. Smaller bikes and bigger canoes allow the bike(s) to be stowed inside the canoe with a lot of creativity, though at best it makes for a heavy boat. Portaging without removing the bike is difficult at best, but the plus side is you can pull out a any point--great for a river with no carries. And like paddling in cold water, the consequences of an upset are high. As always, be sure the boat has sufficient floatation.
Locking the boat and the stuff you don't want to carry:
Cable locks around trees or other roadside attractions have been sufficient so far. Better locks and less desirable (looking) equipment is probably a good idea. Canoe paddles can be locked by wrapping paddle with a cable lock and pulling it tight to a tree or thwart.
Kayaks and kayak paddles pose greater challenges.
Since the world headquarters of HartDesign is on the mighty Hackensack, I've even composed this introduction to canoeing (or kayaking) the Hackensack River.