Some water trails are serviced by outfitters who can provide boats, camping gear, shuttle services to move cars, or other transportation or services. Some of the water trails, however, are "self service", and you need to be able to provide your own shuttle transportation (which includes finding a legal and reasonably secure place to park cars at either end of the run).

The most logical shuttle procedure is for everyone to meet at the put-in (starting point) of the trip, and unload all the boats and gear you will taking.  You then move all the vehicles (with driver only) to the take-out (end of trip), and return to the put-in with only one vehicle (or more if all drivers can't get into one).  At the end of the trip, those whose vehicles are waiting at the take-out must then transport the shuttle car driver (and hopefully all the gear) back to the put-in.

The ideal parking arrangement is to leave the vehicles where someone can look after them.  This could be a paddling rental outfitter, park, campground, business establishment, or even someone's house near the water trail.  You should offer to pay for leaving your cars. There are some places who will have established fees for parking. 

In some cases, it will be unavoidable to leave your vehicles unattended near the water trail.  When leaving cars for several days at water trail parking area, it's a good idea to let local law enforcement officials know about your plans. They appreciate this consideration -- often they are a good source of information about the water trail, and may even provide an added measure of security by looking in on your cars occasionally. They won't guarantee the safety of the vehicles, but at least you will avoid the possibility that they will impound them as abandoned or send out a search party for the missing occupants!