When it comes to overall speed, kayaks have the advantage for several reasons. They sit lower in the water, so there's less wind resistance, which means more speed. It's also clear that the double-bladed paddle is more efficient -- sitting low translates into less time and movement reaching for the water. And because kayak paddles are double-bladed, you don't have to move them from one side to the other like a canoe's single-bladed paddles.
The more of the boat that's in the water, the more resistance it'll meet. Canoes are generally wider and flatter than kayaks, so they tend to have more contact with the water and sit deeper. This means the canoe will have to cut through the water, while the kayak floats on top.
Another consideration is weight and length. The heavier the boat, the more it will sink and, you guessed it -- the more resistance it will face. Longer boats have the weight spread out more and will move faster over the surface. As a rule, sea kayaks are lighter and longer than canoes. The short, sporty kayaks, called rodeo or play kayaks, are made to turn and cut, not travel fast. Sea kayaks are long, lean and fast. Since weight is also an issue, the material used to make the boat has a significant impact on the speed. Both canoes and kayaks can be manufactured from lightweight fiberglass and even lighter Kevlar or carbon-fiber. Kayaks get the edge in this case again because they're narrower and as a result, lighter.
So we've determined that kayaks are generally faster than canoes. But all this hinges on one thing -- whether or not you're a skilled kayaker. If two novice paddlers were to race a kayak and a canoe, chances are the canoe would fly ahead as the kayak zigzagged or spun in a circle. Kayaks are much more difficult for a beginner to keep on a straight line. They're a bit unstable and because they're so light, every time you dig in on the right, your boat will dart left. When you dig back on the left, it will spin to the right. It doesn't take a rocket scientist to figure out that this isn't a very efficient way to move forward.
Because canoes are wider and have more surface area touching the water, they're very stable and glide straight on calm waters. So if you matched up a racing canoe with a racing kayak and had two paddlers of equal strength and experience duke it out on a calm lake, the kayak would be faster. The good news -- canoeists are generally not in a hurry anyway. Otherwise they'd buy a Jet Ski and leave the kayakers in their wake.
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