On a traditional skin-on-frame, the "gunwale boards" are the main structural element of the kayak, forming the upper sides of the kayak. The boards are usually canted at an angle, and this causes the ends of the kayak to rise once the boards are spread apart. The deck beams attach near the top of the gunwales and the ribs attach beneath.
On a composite kayak, the gunwale refers to the same area of the kayak (just beneath the deck seam), but other than some tape for the deck seam, there is usually not a separate structural element.
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