A casually loaded canoe or kayak can make paddling harder and even jeopardize your safety. It may take a bit of experimenting to figure out the right system, but your efforts will pay off in increased convenience, efficiency and safety. Follow these basic rules of thumb to get your own system going:
Make sure your gear is waterproof. Even on the sunniest and calmest of days, some water will collect in the bottom of your boat from wet feet and "paddle drip." Dry bags are made of waterproof, abrasion-resistant fabric and have special sealing closures for watertightness. If you plan to do much portaging, look for ones with shoulder straps. You can also use other packs or duffels, lined with sturdy garbage bags. Avoid packs with large rigid frames: it can be difficult to stuff these into your boat.
Tie everything in. Always important - better to be safe than sorry! Try and develop a simple, repeatable system for keeping everything secure in your boat. If you've got a touring kayak, your gear will probably be kept in closed compartments; make sure those hatches are tight. For open canoes you'll want to make sure your gear is not only tied in, but is secure so it won't shift during the day or dangle if you tip over. Many packs and gear bags come with straps attached: Fasten these around the thwarts, and use a second strap in a criss-cross pattern over and through the whole load. Buckle-end straps work well since they reduce the number of poor or complicated knots to contend with and can be easily tightened later on.
Balance the load. Even a slightly off-balance load can compromise your stability. It can also cause back pain over the course of the day, since you'll unconsciously try to compensate with your own weight. The best balanced loads are trimmed evenly from gunwale to gunwale with heavier items on the bottom for stability. The entire load should be slightly weighted towards the stern.
Do your best to keep your gear below the level of the gunwales, and don't forget to consider the paddler's weight difference in a tandem canoe or double kayak.
Use the ends of the boat only for the lightest gear. Keep your heaviest bags and large water jugs towards the center of the boat, and use the ends for lightweight gear like sleeping bags and pads. The boat will turn and handle much more easily if you keep the ends light.
Keep fragile items safe and organized in dry boxes. Dry boxes are remarkably impact- and water-proof, quick to open and close, and easy to customize with Ensolite or foam. Besides cameras, dry boxes also work well for guidebooks or small supplies that might disappear to the bottom of a dry bag. (Just make sure the dry box can't rattle around in your boat.) Buy ones with the rubber seals in good condition, and before you leave on your trip double-check to make sure the seals are good by loosely wadding paper towels inside and submerging the box in your tub. If the paper towels get wet, you've got a leak. Sometimes a little vegetable oil on the seal will help. Dry boxes are a great solution for packing out garbage and human waste too.
Try to get dry bags in a variety of sizes and colors, including clear. This will go a long way towards improving organization and reducing the frustration of hunting through several bags each time you want something. Try using two or three larger dry bags for camping gear and clothing you won't need during the day. Then, use smaller bags for quick access to lunch, camera, first aid supplies, and other day gear. (If you are paddling a kayak, small bags are probably all you can fit in the boat.)
Keep waterproof day items handy. Sunscreen, sunglasses, compact wind gear, and similar items don't have to go in a dry bag. Try one of the commercially made nylon or mesh seat compartments, or even a fanny pack around your waist for convenient access.
Don't clutter the area around your feet. As tempting as it may be to stuff last-minute items around your legs in a kayak cockpit, or close to your feet in a canoe, try not to; if you tip over, you can get tangled in the excess gear.
Remember, it's hard on you and on your boat to drag it ashore fully loaded. Bring waterproof shoes so you'll feel comfortable unloading the boat from the water. And, of course, carry the empty boat well up onto high ground for the night, especially on a river or tidal area where water level fluctuations can take you by surprise. Turn your boat over to keep rain out and to make it harder for an unexpected gust of wind to catch it.