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Structural Design and Materials
Large pontoon boats typically have aluminum or fiberglass tube-like hulls that span the width of the boat. Some have bi-toon or tri-toon classifications, meaning two or three pontoon hulls. The inflatable pontoon has a double tube-like hull, but in many cases lacks the large deck area, possessing only a single or double seat arrangement. Kayaks can be made of aluminum, wood or fiberglass, and are typically smaller than pontoon boats, with the exception of the inflatable variety. Kayaks have a single hull of solid material or can be completely inflatable. Both inflatable designs can have aluminum or wooden folding frames.
Portability
The pontoon boat, because of its rectangular profile and extra width, is less portable the larger it gets. Many of the larger pontoon boats, even the inflatables, must be transported by trailer because of their increased size and weight. Kayaks lend themselves well to roof-top and truck-bed transportation because of their narrower width and lighter weight.
Engine Power
Pontoon boats with solid construction offer the best choice for powered outboard, stern-drive or outboard engines. Pontoons have no real limit for size and horsepower, if the transom area is strong enough to support the weight and torque. The smaller inflatable pontoon boats can accept only the smallest of outboard motors. Kayaks typically have little options for motor installation, except when they have flat transom designs or bow decks that can accommodate electric trolling motors.
Stability and Capacity
The larger pontoon boats have exceptional stability due to their width and double pontoon flotation. Large pontoon boats resist rocking or tipping even in rough water and can hold up to 15 passengers in comfort. The smaller inflatable pontoon boats also have secure stability characteristics, but their seating is limited to one or two occupants. Large kayaks can hold up to three, sometimes four people, with limited storage for gear. Due to their decreased width, kayaks have tipping and flipping issues, and are more prone to instability in rough waters.
Rough Water
Large pontoon boats, because of their larger profile, do well in rough weather, but can be influenced by strong currents and high winds. However, inflatable pontoon boats perform poorly in fast-moving streams and rivers due to their large hull areas and rectangular design. Pontoons boats must be rated for certain white water conditions so they do not exceed their structural limitations. Kayaks of any size excel in the roughest white water conditions due to their sharp profiles and high maneuverability. Kayaks also maintain the fastest speeds in heavy currents or white water.
Ease of Use and Versatility
Pontoon boats have a tendency to be sluggish or slow in the water, even with the smaller designs. They can not turn as sharply or react as quickly as the sleeker kayak. Pontoon boats require more handling skill, both in operating and in anchoring or beaching. Kayaks handle well, even with solo pilots; they turn and react almost instantly and can be paddled much faster than pontoon boats. An individual can beach a kayak with limited effort and time expended.