Start removing shingles in the suspect area. Once removed, evidence of the leak becomes visible and you can track it right to the source. Discolored felt paper or water-stained — even rotted — wood shows up directly below and around leak.
25 Ways to Fix Gutter Leaks and Other Roofing Issues

Solution for a Small Leak
Sometimes you can’t find a leak because the water shows up at a ceiling spot distant from the problem spot. If your ceiling has a plastic vapor barrier between the drywall and the attic insulation, push the insulation aside and look for flow stains on the plastic. Often water runs to openings in the vapor barrier, such as at ceiling light fixtures.
If you can’t see any telltale flow marks, and because the stain is fairly small, look at the underside of the roof for ‘shiners.’ A shiner is a nail that missed the framing member — in this case, when the carpenter nailed the roof sheathing to the rafters.
Moisture that escapes into the cold attic from the rooms below often condenses on cold nails. Sometimes you can spot this if you climb up into your attic on a cold night. The nails appear white because they’re frosted.
When the attic heats up a bit during the day, the frost melts and drips, then the nails frost up at night again, and so on. Simply clip the offending nail with a side-cutting pliers.

Fix Plumbing Vent Boots
You’ll find plumbing vent boots made entirely from plastic, plastic and metal, or even two-piece metal units. Check plastic bases for cracks and metal bases for broken seams. Then examine the rubber boot surrounding the pipe. That can rot away or become torn, both of which allow water to work its way into the house along the pipe. With any of these problems, you should buy a new vent boot to replace the old one.
If you see missing nails at the base or find some that have pulled free you can replace them with the rubber-washered screws used for metal roofing systems — if the boot is in good shape. You can get them at any home center, located with the rest of the screws.
To replace a roof vent, you have to work the neighboring shingles free on both sides. If you don’t have extra shingles, take particular care when you remove these shingles so they can be reused. Use a flat bar or putty knife to separate the sealant between the layers. Then you can drive a flat bar under the nail heads to pop out the nails.

How to Fix Roof Vents
Check for cracked housings on plastic roof vents and broken seams on metal ones. You might be tempted to throw caulk at the problem, but that solution won’t last long; you must replace the damaged vents.
Also, look for pulled or missing nails along the base’s bottom edge. Replace them with rubber-washered screws. In most cases, you can remove nails under the shingles on both sides of the vent to pull it free. You should find nails across the top of the vent, too.
Usually you can also work those loose without removing shingles. Screw the bottom in place with rubber-washered screws. Squeeze out a bead of caulk beneath the shingles on both sides of the vent to hold the shingles down and to add a water barrier — a much easier task than renailing the shingles.

Fix Walls and Dormers

Complex Roof Problem
This roof leaks during the snowy part of winter and during storms in the summer, certainly because of poor flashing. The soffit that meets the roof is one of the toughest areas to waterproof. In the photo, you can still see signs of an ice dam. An ice dam occurs when snow melts and the water refreezes as it hits the colder edges of the roof. Eventually, water pools behind the dam and works its way back up under the shingles and under the soffit until it finds an opening through the roof.
The solution begins with good flashing, as this should stop leaks from rainfall and might stop the leaks from ice dams, as well. Begin by removing the shingles down to the wood sheathing and slip a strip of adhesive ice-and-water barrier (available where roofing repair products are sold) under the soffit/main roof joint.
Depending on how the roofs join, you may have to cut a slot to work it in far enough. It should overlap another piece of ice-and-water barrier laid below, all the way down to the roof edge. Doing this should cover the most leak-prone areas.
Then reshingle, sliding metal step flashing behind the fascia board (the trim behind the gutter). The valley flashing, laid over the joint where the two roofs meet, should overlap the step flashing at least 2 in. If leaks continue to occur from ice dams, consider installing roof-edge heating cables.
Improved attic insulation and ventilation usually provide the best strategy to prevent ice dams, but they may not resolve this complicated leaky-roof situation.

Fix Step Flashing
You find step flashing used along walls that intersect the roof. Each short section of flashing channels water over the shingle downhill from it. But if the flashing rusts through, or a piece comes loose, water will run right behind it, and into the house it goes. Rusted flashing needs to be replaced.
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