On the water
Figure out standard places to stow gear on or in your boat, including how many and what size dry bags or other gear containers you need. Once you've developed your packing system, label the bags with where they go in your boat and what they contain, for example, bow, spare clothes; aft bulkhead, cooking gear. (While you're at it, mark the bags with your name and phone number.)

I always carry one or two flotsam bags on kayak trips. They are nylon mesh bags with carry handles - the kind sold as reusable grocery bags. I've found that, even with a variety of gear storage systems, my cockpit carries a variety of flotsam on every trip: snack bags, water bottle, sunscreen, boat horn, etc. I use flotsam bags for carrying that gear to and from the boat and generally containing it. On a five-week trip in Prince William Sound, Alaska, I used a flotsam bag for carrying my thermos, water bottle, snack bag, seat cushion, and neoprene mukluks to and from the boat. The last stage of packing was to take off my heavy rubber boots, put on the mukluks, stow the boots and all the flotsam, then hop in the boat. Having the right size and quantity bags and a boat-loading routine streamlines the tasks at the launch site and when unloading at a campsite. Before going out on a trip in a new boat, take some time in the backyard or somewhere else where you can really figure out the optimal way to load your gear. When you're packing at the end of the day or the end of the trip, put gear back into the same bags. You'll save time and have more room if you develop a reliable system and stick to it.

Using a standard boat-packing system can also serve as a good backup to check that you have all of your gear. I figured this out when I got to the end of the first day of a three-day solo trip in Maine and realized I'd left my food bag in my car. I had been really proud of myself when I packed my boat at six that morning because it seemed as though there was lots of extra room in the boat. The food bag left buried in the car was the reason for the extra room. Now packing my boat allows me a chance to review what gear I have with me. Extra room is no longer reason to pat myself on the back for packing so efficiently - it is my cue to double check the gear lists and gear bags.