Why Is My Skylight Leaking? Seal, Flashing or Condensation

Updated 2026-10-24 · Sources checked

"This morning we had a really hard rain and the skylight is leaking."

A homeowner who started a thread on r/Roofing wrote that. The water can be condensation, a failed glass unit or flashing that has let go. When and where it shows tells you which to suspect. Drips on cold mornings can be condensation, because the colder it is outside, the greater the chance of condensation inside¹. Fog between the two panes means the glass unit has failed². Water after rain is coming in from outside, for example around the flashing, the metal strips that seal the skylight to the roof.

Is the leak right above the stain?

Usually not. Leaks are rarely located directly above the water spot on the ceiling⁴, so the wet patch near the skylight may be far from where the water gets in. That is why a repair aimed at the stain can miss.

As one commenter in a roofing thread put it, "In my opinion Skylights are not easy too diagnose the leak." The checks below are how you get a better description to hand to a roofer.

The order to follow when you cannot find the leak

1. Find where the water comes from. Note when it shows and where, then do the checks in the next section.
2. Protect the house. Catch the water, move belongings away and take photos before you change anything.
3. Hand your notes to a roofer you choose, with the questions further down.

Not sure the water is from the skylight at all, or who should trace it? Who to call for a roof leak.

Check it without going on the roof

Stay off the roof: a professional roofing contractor should do the closer assessment and the repairs⁵. The garden-hose water test some people suggest is work for someone experienced in enclosure forensics⁶, so leave it to a pro.

What to look for, and where:

• Inside: peeling paint and water stains on the framing⁷ around the skylight.
• From the ground, with binoculars: flashing that looks corroded, pulled loose or cracked⁸. Binoculars give a closer view⁴ than the naked eye.
• In the attic: a drip trail⁴ running from the skylight area.
• On the glass: condensation between the inner and outer panes² of the sealed glass unit.

Write down what you find. Those notes are what the roofer needs.

Which sign points to which fix?

• Stains after rain, a drip trail in the attic or damaged-looking flashing: the flashing is the suspect, and a roofer you choose can check it.
• Drips on cold mornings and none in rain: cold weather raises the chance of condensation¹, so tell the roofer it may not be rain coming in.
• Fog between the panes: a failed insulated glass unit is a unit problem, not a flashing problem², so new flashing alone would not clear it.

In cold weather, could the water be coming from inside the house, not the roof? Condensation in the attic versus a leak.

Why can caulk where the water shows miss the problem?

A skylight is a built-in weak spot. Weathering of components and improper installation can lessen the effectiveness of the water control layers⁶ around it, and flashing can corrode, pull loose or crack⁸. Sealant dabbed where the stain sits treats none of that, so it may not settle the leak.

Ask the roofer, in writing, for the repair price and for how long the seal should last, as below.

While you wait: if the roofer can't come today

• Water coming in now: put a bucket under it, lay towels and move furniture. Dry water-damaged areas and items within 24-48 hours³ to prevent mold growth.
• If you may file a claim, take reasonable steps to protect your property from further damage and save receipts⁹ for what you spend.
• After the next rain, check again from the ground and the attic for a drip trail⁴, and add it to your notes.

Can the roofer just fix the skylight leak, or does the skylight need replacing?

The answer depends on what the roofer finds, and checking for leaks and water damage is the step that decides it². Ask the roofer for a photo of every problem they find, from the flashing and the glass unit to any rot in the area around the leak.

Then get it in writing: a quote that lists flashing work and skylight replacement as separate items, and what they would do and charge if they find damaged wood. You can send this:

Please write in your estimate what is wrong with the skylight, what you will repair or replace for each, and the price of any extra work if you find rotted wood. Please also send photos of each problem. Please say in writing whether you will come back at no charge if this same leak returns, and for how long.

If a roofer won't put this in writing, that is an answer too: weigh it against the bids that do.

A homeowner who started a thread on r/Roofing about a friend's new roof wrote, "neither of us are certain what to say to get them to do it right." Your notes and the written quote give you the words.

Is resealing enough if the flashing turns out to be the weak spot? Can roof flashing be repaired or does it need replacing.

Quick questions

What causes condensation on a skylight?

Humidity is one cause: condensation can be a sign of high humidity³, so dry the wet surface and reduce the moisture source. Mention the dates of the drips to the roofer, so they can tell condensation from a leak.

Do skylights need to be resealed?

It depends on the condition of the sealant and the flashing. Ask the roofer to check them and tell you, in writing, what they see and what they would redo.

How can you prevent a leaking skylight?

Weathering wears down the layers that keep water out, so ask for the skylight flashing to be looked at whenever a roofer is already working on your roof. Early signs are the peeling paint and stains you can check from inside.

If the roofer's repair doesn't stop the leak, will you have to pay to have it fixed?

That depends on what you agreed. Read the estimate or contract for what it says about leaks after the work, and ask before signing if it says nothing.

Sources

1. NDSU Extension, Window condensation a common problem

2. U.S. Department of Energy, Replacing Existing Skylights

3. U.S. EPA, A Brief Guide to Mold, Moisture and Your Home

4. University of Wisconsin-Extension, Assessing and Repairing Leaky Roofs

5. NRCA, Roof Repairs After a Storm

6. Pacific Northwest National Laboratory (U.S. Department of Energy), Existing Skylights Repaired or Replaced and Fully Flashed

7. U.S. Department of Energy, Inspecting Skylights for Water Damage and Infiltration

8. IBHS, Extend the Life of Your Roof Through Routine Maintenance

9. Triple-I, Settling insurance claims after a disaster

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