Whether you own a pair of Simms Gore-tex, Patagonia breathables or a vintage pair of neoprene waders fixing the problem is relatively easy.
First let's talk about breathable waders like Patagonia and Simms. To find the pin holes causing the problem you need to completely dry your waders inside and out. If you are fresh off the water it is completely safe to put your waders in the dryer. Just be sure to snap all the buckles and have your dryer set on low heat. Once dry, turn your waders inside out. Take a spray bottle filled with rubbing alcohol and liberally spray the inside of your waders. Wherever you have a pin hole leak it will show up as a dark spot on your waders in a matter of seconds. I am always surprised by the number of pin hole leaks in the waders when I repair them. There always seems to be quite a few more than expected. Using a tube of Aquaseal, squeeze out a dab on the pin hole and rub in with your finger. Repeat as necessary. Let dry for at least 12 hours and that is all you need to do to repair pin hole leaks in your breathable waders.
If your leak is in the neoprene bootie you will need to fill your waders with water (fill only to knees) and roll your waders down and try to find where the leaks are. Use something to mark the areas to be repaired, drain and dry. Use an ample supply of Aquaseal to the leaky area and work into the neoprene. Problem fixed. If there is a leak in any of the seams you should return your waders to the manufacturer for a professional repair job.
Repairing Pinholes in Your Waders
Stockingfoot Repair on a Simms Wader
To repair any neoprene waders you may need to fill your waders with water to find the leak but in most cases the leak should be easy to find. Look for tears, or punctures in the material. You then can apply a liberal amount of Aquaseal or SG-20 (a flexible epoxy like material) to the leaky area to seal it again. I haven't used SG-20 personally but have heard enough great reviews that I believe it to be a good product for this application. It is a dark brown material and not quite as sexy looking as the clear Aquaseal. But, it only takes an hour to cure versus the recommended 12 hrs for Aquaseal.
Another great product for an on the water fix is from Loon products. It is called Loon UV wader repair. I was guiding the Missouri river one late fall and because of the cold weather I had a small portable heater going in the boat by my feet. I only noticed a problem when a foul smell hit my nose. I looked down at my waders and two inches up from my boots there was a hole melting about the size of a dime. I whipped out this small tube of sealant squirted it all over the hole, exposed it to the sun for a few minutes to cure and they never leaked again. I was pleasantly surprised by this quick fix and highly recommend having a tube of this stuff handy for emergencies like the one mentioned here.