Skylight Leaks in Alpharetta: 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 the second most common leak we're called to in Windward, Medlock Bridge and the older Crabapple streets, after 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. This is 70% of skylight leaks. 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, we lift the shingles around the unit, check the flashing laps, look for the caulk-only joints, and run 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. Every skylight leak repair Alpharetta homeowners call about on a roof less than five years old is 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.
HOA note
Replacing a skylight like-for-like doesn't need approval anywhere we work. Adding one, or changing to a larger unit, usually does in Alpharetta and Milton subdivisions with architectural review, because it changes the roof elevation. We 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 we find it and what the written price looks 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?
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