Before going out to the store to purchase a fishing kayak, think about the bodies of water you are most likely to paddle in, in what conditions you intend to fish, and how much you have to spend on the boat. There are two general fishing kayak categories: sit-in and sit-on-top. Sit-in kayaks are great for trips in cold water, and longer trips that require more stability. Sit-on-top models allow the paddler to access equipment more easily, and to get in and out of the boat quickly and easily, even while floating in the water.
Each type of kayak has its own set of advantages and disadvantages. You should choose which fishing kayak is best for you by considering the ways in which you will be using the kayak most of the time. Think about whether you want a kayak that you will paddle, or one that you will pedal. Pedal kayaks are more expensive, but they free up your hands for more efficient fishing, and they can be easier to propel forward on long trips. Paddle kayaks are the more traditional choices, and they offer stability and control while paddling. Paddle kayaks tend to be less expensive, though you will need to still buy a paddle for a pedal kayak in case the pedaling function breaks down for any reason.
Consider the rigging of the fishing kayak as well. A fishing kayak must feature some sort of holder for your fishing rod, and other rigging can help secure other fishing equipment that you will need while out on the water. Make sure the rigging is easy to access from the sitting position, even if you have chosen a sit-on-top kayak. You should be able to access your equipment without having to move too much, which can potentially cause the boat to become unstable.
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Think about the size of the boat as well. A long, thin fishing kayak will move more quickly through the water, and it will be more likely to go straight through the water. A shorter, wider fishing kayak will be more stable, though it will not move as fast through the water and may not go as straight. If stability is important to you, particularly if you are a beginner kayaker, a shorter, wider boat may be the best choice. The experienced kayaker will probably want to choose a longer, narrower kayak to ensure ease of use and a faster movement through the water.