This is no time to put the kayak away. In fact I paddle more in the fall and winter than I do in the summer. The reasons are many. The water is empty and quiet. The trees look amazing. And most importantly - not really - your friends will think you are hardcore.
But if you are going to paddle in the fall and winter you need to do it safely, which means dressing for the environment. There is one big debate that rages back and forth about, and that debate is, do you dress for 'submersion' or not. Honestly, I think either one can work. If you are careful and take some precautions.
My first choice for winter paddling is a drysuit. I absolutely love my Kokatat GMER. I have used it for about 4 or 5 years now, and it has been sensational. But the price tag is a little high for most recreational paddlers ($1030 US at NRSWEB.com). The gaskets at the neck and wrists are the best I have ever seen, they are silky soft and hold up well. That said, if you want to make fall and winter paddling - or you paddle someplace that always has cold water, like Alaska - then it is the premier choice. There is no safer, more comfortable way to paddle in a world of cold water and cold air.
Your next option down the chain in terms of price range is a combination of a dry top, and dry pants. If I were going to do it today, because I have good experience with Kokatat products I would go with The Rogue Top ($430 at backcountry.com) and Tempest pants with socks ($180 at REI.com).
Yes, you are still a little over $600 for this pair, but they are offering you awesome protection. While I haven't used the Rogue top I am sure it has very similar silky gaskets and the same quality I have come to expect from Kokatat. I think the most important thing about the pants, are the socks which I should point out are connected to the leg of the pant the same way they are in the drysuits. This is super important, and was my main reason to move into a drysuit, as it allows you to launch your boat without getting your feet wet. Slip your regular paddling shoes or sandals over them, to protect them.
But maybe $600 is too much for you to spend on paddle specific clothing? What if I told you you probably already have clothing that works, that could be used in a kayaking environment? If you read this blog, you know that I stopped using a loved Patagonia Skanorak paddling jacket in favor of an REI eVent rain shell. You can absolutely use standard rain wear, with just a couple of precautions. They work beautifully on top of the water, but if for some reason you end up in the water unexpectedly, then you have a problem. Which means you need to be prepared once you get back into your kayak to fix this problem. When I am in this situation - and I was about 5 years ago - pre drysuit - I paddled to shore, changed into dry clothes and made a hot, sugary drink with a jet boil. You may want to be prepared to do this in the boat if you can. Which means dry clothes in a drybag, in the cockpit. This isn't ideal, but this can definitely be done. I did it for a long time before making the drysuit plunge. Just think through what it is you are going to do, if the worst happens. (Don't paddle alone, and tell people when you are going, and when you will return).
I want to talk quickly about feet, because they will definitely be in the water, and if you aren't doing pants or a drysuit with socks, think about something like this, or this. They will keep your feet warm and dry getting into and out of your boat. Which is key to a pleasant paddling day.
Speaking of warm and dry, all of these options I have discussed are essentially shell layers. You are going to have to find base layers underneath to keep you warm, particularly when you are in the water. I used the Patagonia capilene 4 (heavyweight) when I used a dry top and pant in Alaska, but I found that layer too warm for under a drysuit and switched to Cap 3 with a crew neck. A few years ago I switched again to REI powerdry, which works just as well, has a nicer hand feel, and costs less. It was a grey powerdry top that I wore for 21 days on the Inside Passage. I would also add that a big part of this is finding what works well for you, and adapting what you see other people doing. If you paddle in groups always look around at the paddlers around you I guarantee you will pick things up.
Having had the experience of doing a NOLS instructor course, a WMI instructor course and a couple of other similar courses, I think I have learned more from my fellow instructors, in just seeing how they do things. Learn from those around you. I have talked before about having 'a beginners mind' - which means simply you are open to learning new things. Continue to learn something new everyday. Particularly every day on the water!