Waterproof fabric is used to make tents, awnings, garments and outdoor furniture, but untreated thread is often used when the items are being manufactured. This thread decays, leaving behind a waterproof item with a leaky seam. There is a secret to sewing on waterproof fabric and making it last. Buy thread that has been treated with ultraviolet protection, which will make your seam repair last as long as the waterproof fabric.
Trim any frayed threads off of the raw edge of the damaged seam. The seam will not hold if you sew on frayed fabric. Cut as close to the raw edge as you can.
Look at the original seam. Fold the raw edge the same way it was folded when you started. If you run into a problem and cannot get it to go back the way it was when you started, it needs to at least overlap the bottom layer of fabric. Pin the folds with the straight pins.
Put the ultraviolet-protected thread on the sewing machine and set the machine on a medium-length straight stitch.
Align the sewing machine needle with the original seam at least 2 inches before the open spot. Sew directly on top of the original seam, across the opening and at least 2 inches past the end of the opening. This is called top stitching because it is visible from the top of the fabric. The thread line will be secured by the overlapping thread.
Move the needle to the other line of stitches and repeat step 4 on the second line of top stitching.
If you want extra waterproofing, buy a stick or tube of waterproofing at camping or sewing supply stores. Ultraviolet-protected thread is available at upholstery shops, upholstery suppliers and stores that sell outdoor canvas.