So you have a leak and have narrowed the problem to "there's a hole in the roof" (which might go something like this: "it leaks everytime it rains, there's a hole in the roof").
What you'll need:

-Tar (for rain and sunny weather ("wet+dry"))
-A roll of fiberglass netting (wet+dry preferably)
-Trowel, scraper, or stick that you'll never use again except solely for more tar involved jobs.

Step 1
Go directly above where the leak is on the roof and look around for a crack or a place where there might be a crack.

Step 2
Put a "glop" of tar over the crack, make sure it's enough to completely cover the whole and a piece of fiberglass netting (and then some). Spread it out evenly, but doesn't have to be perfect.

Step 3
Cut out enough netting to cover the crack and about 2-4 inches. Place the netting on top of the tar.

Step 4
Put another coat of tar on top of the netting so that you can't see any of it at all.

In about 2-3 years the tar should be dry. The fiberglass will keep the tar from cracking in the future as well (often overlooked by lots of people). To get any tar off of yourself just use some paint thinner or you could even use gasoline to rub it off.

Roofs develop leaks. Neglecting these leaks, even for the short period of time it takes to locate a competent roofer and convince him to re-roof your house, can result in problems. Water is an anathema to the framing structures in the attic space. This moisture, combined with the close, warm conditions found in the attic space of most houses, will encourage the growth of mold, dryrot, and insects. Even if you find a roofer to repair the leak or replace the entire roof before any damage is done to the framing or the roof deck, the moldy conditions can make life miserable for anyone living in your house.

Why roofs leak

Built-up roofing, made of layers of roll roofing, is an inexpensive way to roof a structure when appearance isn't important. The useful lifespan of this type of roof varies according to several factors. The more layers used to construct a roof of this type, the longer the roof will remain leak-free. A six-ply roof should last longer than a three-ply roof. A roof covered with a protective coating, such as gravel or reflective aluminum paint, should have an appreciably longer lifespan than one that is at the mercy of the elements. Walking on your roof will damage it and shorten its life. It may seem like a good idea to haul a cooler full of beer up to the roof and watch the summer fireworks display, but roofs are not made for walking upon, and it is almost certain that damage will occur. The framing members used to support a roof are not as substantial as those that make up a floor, and flexing caused by a person's weight will damage the roof to some extent. Flexing can cause nailheads to loosen and poke through the roof. It can also cause bubbles to form and fishmouths (wrinkles at a seam) to open up. Water is insidious. If there is a way, it will find its way through your roof. You never know when a driving rainstorm will open a seam, or when an errant football will bounce off just the wrong part of your roof.

How to patch a leak

It can be difficult to tell where a leak is coming from, but if you think you know where the leak is, you can try to patch it. If at all possible, do this work when the roof is dry, on a day that is well above freezing. You will need a tub of roofing cement or roofing tar. A disposable brush or something similar is essential to spread the tar around. You may also need fiberglass tape impregnated with asphalt. Roll roofing, which can be made of felt, fiberglass, or asbestos impregnated with asphalt, may be used to cover the repaired area.

If it is obvious that there is a nailhead poking through the roof, you can try to extract it without causing further damage to the roof. Use a claw hammer or a pair of pliers and get a grip on the nailhead. Place a piece of wood under the hammer so that you are not levering against the roof surface. If you think you can't remove the nail without pulling the roof layers apart, you can try to press or hammer it back into place. Be judicious with your use of the hammer. Often, a leak will soften the roof deck and hammering might do more harm then good. A roofing hammer with a broad head will minimize the damage caused by missing the nailhead. Use a healthy dollop of tar and try to work it into the nailhole if you can do so without further disturbing the area. If there is an actual gap where the nail was, you can use a wadded-up piece of the fiberglass tape to fill the hole and retain the tar. After sealing the hole, lap tar around the damaged area, and cover it all with a piece of roll roofing. Press this roll roofing into the tar and make sure the edges are all flush with the roof surface. Cut this patch so that it is at least six inches from the hole on all sides. Such a patch should be flattened by laying it in the sun for a few minutes until it loses the curve from being rolled. Round the edges of the patch.

If the leak is a result of a bubble on the roof where the layers of roofing have separated, you will need to carefully cut a cross in the top layer of the bubble with a sharp utility knife. Needless to say, avoid any unnecessary damage to the roofing material under the bubble. Next, carefully peel these layers back and glop as much tar in there as is practical. Replace the layers that you peeled back and lap tar over the entire area, patching it with a layer of roll roofing that extends six inches from every edge of the cuts that you made to flatten the bubble. If a seam has wrinked, resulting in a fishmouth leak, you can slit the fishmouth down its length, then peel each side back and seal with tar before closing the fishmouth and pressing it flat. Patch with a piece of roll roofing in the same manner that you would fix a bubble leak.

In the unfortunate case of leaks around skylights, smokestacks, parapet edges, or other similar structures, you will have to apply layer upon layer of fiberglass tape and roofing tar. This is a messy job, and is not always successful.

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