Skylight Leaks in Alpharetta: Repair the Flashing or the Unit?
Skylights were a builder's favorite in the 1990s subdivisions here — a bonus room over the garage with two of them, a master bath with one, a kitchen with a bank of three. Thirty years on, they are one of the most common leak sources in Windward, Medlock Bridge and the older Crabapple streets, along with pipe boots. The good news is that most skylight leaks are not the skylight. Here's how to tell what you have.
The three things that leak
The flashing kit. A skylight sits in a curb or a frame, and a set of metal flashings — a sill piece, step flashings up each side, a head piece at the top — weaves it into the shingles. On a 1990s install the kit was often a generic aluminum set with the joints caulked, and the caulk is long gone. Water gets under the step flashing or over the back of the head flashing and runs down the well. Most skylight leaks are the flashing kit, not the glass. If you're wondering how to seal a skylight roof leak yourself, fresh caulk over the old joints is a stopgap, not a fix. Fix: a new manufacturer flashing kit installed with ice-and-water membrane under it, $400–$900.
The unit's seal. Double-pane skylights have a seal around the edge of the glass. When it fails, moisture gets between the panes — you'll see fogging or condensation you can't wipe off — and, on the cheaper units, water finds its way through the frame. Fix: replace the unit, $1,200–$2,500 installed including new flashing.
The curb and the roof around it. On a steep roof, water piles up on the uphill side of the skylight. If the shingles there are worn or the original installer didn't put a diverter or a cricket behind a wide unit, the water sits and finds a way in. Fix: rebuild the uphill flashing with membrane and, on units over 30 inches wide, a small cricket. $500–$1,000.
How to tell which one you have
From inside, look at where the water is showing up in the skylight well — the drywall tunnel between the ceiling and the glass.
- Stain at the top corners of the well, or across the top: head flashing or the roof above. Flashing kit.
- Stain down one side: step flashing on that side. Flashing kit.
- Stain at the bottom, or water on the glass inside: could be the unit's seal, or could be condensation.
- Fogging between the panes: unit seal. Even if it isn't leaking yet, it's done.
- Water only after a windy storm from one direction: flashing on the windward side.
- Water only on cold mornings, no rain: condensation on the inside of the glass, not a leak. Common in bathrooms with a skylight and a weak exhaust fan.
From the roof, a roofer lifts the shingles around the unit, checks the flashing laps, looks for caulk-only joints, and runs a hose at each edge in turn while someone watches inside. Twenty minutes usually settles it.
Why they fail here
Georgia sun and heat. The caulk in a 1990s flashing kit is gone within 10 years. The rubber gaskets on the unit dry out in an attic-adjacent well that runs 120 degrees in summer. Pine needles collect on the uphill side and hold water against the head flashing all year. And thunderstorm wind drives rain uphill under the shingles above the skylight, where the original underlayment was a single strip of felt.
Repair or replace the unit?
| Situation | Answer | Cost |
|---|---|---|
| Leak at flashing, glass clear, unit under 20 years | New flashing kit | $400–$900 |
| Fogged glass, any age | Replace unit | $1,200–$2,500 |
| Unit over 25 years, flashing failing | Replace unit — you're paying for the flashing labor anyway | $1,200–$2,500 |
| Roof is being replaced within 2 years | Wait and replace the unit during the re-roof | Adds $800–$1,800 per unit to the roof job |
| Roof being replaced now, skylight works | Replace it anyway | Same |
That last row is the one people push back on, so here's the reasoning. A new roof lasts 20 years. A 25-year-old skylight will not. If you keep it, you'll be paying a roofer to come back and cut into a new roof in five years. A lot of the skylight leak repair Alpharetta homeowners need on a roof less than five years old traces back to a skylight that was kept during the re-roof.
Removing one instead
Some homeowners decide the bonus-room skylights that leaked twice are not worth keeping. Removing a skylight during a replacement — decking the opening, tying in the shingles, and drywalling the well inside — is $600–$1,200 per unit. Worth considering on a north-facing roof where the light was never much anyway.
What a skylight leak repair involves
A proper flashing repair is more than new caulk. Here's the usual sequence on a shingle roof:
- The shingles around the skylight are lifted or removed, back to the first full course on each side.
- The old flashing pieces come off, and the curb and the decking around it are checked for rot.
- Ice-and-water membrane goes on around the curb, lapped so water runs over it, not under.
- A new flashing kit, ideally the one the skylight maker sells for that model, goes on in order: sill, steps, head.
- The shingles are woven back in and sealed, and the hose test is run again.
On most units it's a few hours' work. If the curb is rotten, add time and a decking charge.
Questions to ask about the repair
- Is the leak at the flashing, the glass seal, or the roof above?
- Will you use the manufacturer's flashing kit or a site-built one?
- Is there rot in the curb or the decking, and how will you price it?
- How old is the unit, and is it worth keeping under this roof?
- Will you photograph the old flashing when it comes off?
Living with an older skylight
If you keep a 1990s unit for now, a little care helps. Clear pine needles from the uphill side each fall. Check the well inside after the first long winter rain. Run the bathroom fan longer if the glass fogs on cold mornings. And keep an eye on the corners of the well; a faint stain there is the early warning before a drip.
Common questions
Can I fix a skylight leak with sealant from the hardware store?
As a stopgap, sometimes. Sealant on the joints of an old flashing kit may stop a drip for a season. It won't last in Georgia sun, and it can trap water if it's put on the wrong side of a lap.
Why does my skylight only leak in heavy storms?
Wind. Driving rain gets pushed up under the head flashing or the shingles above the unit. Light rain runs off without finding the gap.
Is a leaking skylight an insurance claim?
Usually not. Worn flashing is maintenance. If a storm cracked the glass or a limb hit the unit, call your agent and photograph it first.
How long does a new flashing kit last?
A manufacturer kit installed with membrane underneath should last as long as the shingles around it. That's a good reason to replace the kit when you replace the roof.
HOA note
Replacing a skylight like-for-like usually doesn't need HOA approval — check your covenants. Adding one, or changing to a larger unit, usually does in Alpharetta and Milton subdivisions with architectural review, because it changes the roof elevation. Ask the roofer to include it in the submittal if it's part of a replacement.
If you have a stain in a skylight well, the roof repair page covers how a roofer finds it and what a written price should look like. If the roof is 20-plus and the skylights are original, the decision belongs in the replacement conversation, not a repair one.
Need roof work in Alpharetta?
Call for a free estimate. Mon–Sat 7am–7pm.