I work for Pamlico Sea Base ( http://pamlicoseabase.org ) as a sea kayaking guide. One of our trailers is built for canoes and doesn't have fenders over the tires. Unfortunately someone wasn't paying attention when loading it with kayaks and the sides of a few boats sat on the tire for a 2 hour trip. We now have 3 boats with gaping holes in them.
It isn't very likely that you'll have a kayak with such a large hole, but whatever the size, here's how to fix it.
Step 1: Materials and Tools
1. some sort of patch. we had an old trashed boat we could cut up. The only other plastic I know that will stick well are those big blue 50 gallon drum/barrels. Make sure you wash it out well!
3. heat gun (I used a blow torch which isn't great but works)
4. a water bottle (for safety reasons)
5. a large metal spoon or putty knife
6. a pair of pliers
Step 2: Prepping the Kayak and the Patch
Sand the edges of the patch and the edges of the hole. I used a grinder for the patch to make things go faster. (I had 3 boats with holes in them) Some people will tell you to sand the side of the patch that will stick to the boat and the plastic of the boat around the hole the patch with attach to. I don't know if this helps the patch stick or not because I didn't bother doing it. It's probably worth trying.
If the hole is next to the seat or any rigging or anything that would either get in the way or catch fire, remove it. For the boat pictured, we had to take the seat out, take the paddle holder off, and move the rudder cable.
Step 3: Attaching the Patch
This is truly the hardest part. I needed assistance because you have to move very quickly.
set up your work space so that everything is accessible.
1. put on your gloves
2. turn on the heat gun or ignite the torch
3. with the pliers, hold the patch at a corner
4. using the torch/gun, melt the patch to the point that it is droopy but be careful not to burn a hole in it. Its easy to burn a hole through it with a torch. A little harder with the gun. I use slow sweeping motions across the body of the patch
5. sweep the torch across the outer edges of the hole enough so that the plastic starts to turn a different color. This boat turned yellow when it was ready, others turn white. be careful not to stay in one place for too long or you'll have two holes instead of one!
6. you have to work EXTREMELY quickly, while both the patch and the boat are still hot. The patch needs to be pretty droopy and the boat sticky. you'll have to hold the patch in your hands and press it to the boat. Even with gloves on it gets a bit hot!
Step 4: Smoothing Things Out
Now that the patch is on, you need to make sure it'll stay on, hold water and look a bit better. This means you'll need to smooth things out. this part is really all about trial and error. It took me a good 15 minutes to get the technique down. Here's what to do.
1. get your torch and metal spoon or putty knife
2. frequently the edges of the patch won't be stuck to the boat even if the patch is staying stuck to the boat, I held the torch so that the flame went between the edge of the patch and the side of the boat until both turned yellow then I pressed them together using my gloved hand or the spoon.
3. to smooth things out: heat up a small area (4 square inches) at the edge of the patch until it turns a color but not to the point that it catches on fire
4. with small sweeping and frequent strokes, sweep the melted plastic of the patch out onto the sides of the boat. move quickly. as the plastic cools, or if you press too hard, the plastic with stick to the spoon. I would frequently wipe the hardened plastic off the back of the spoon using the cinder block
5. it is best to heat up a small section and focus on it until you are satisfied with the smoothness and then move on. don't heat up a long section and try to work because it cools too quickly
6. I turned the boat over and propped it up on a cinder block for better access to the bottom of the patch
Step 5: Almost Finished
Put the boat up on some saw horses if you have them and pour water into the cockpit. Watch for drops of water to come out of the patch. Work these areas over again with the torch.
Now if you want to, you can use the torch on the inside of the boat to transition the plastic of the boat to the patch. This time you're smoothing the plastic of the boat onto the patch. I think this step isn't very necessary unless your patch is leaking.
Now all you need to do is sand the patch smooth. Unfortunately my boss never got around to bringing me a sander so our boats are a little rough.
After you sand the patch smooth, reattach all your components and you're ready to paddle!