Why Is My Skylight Leaking? (5 Causes, Ranked)

Most Likely Causes (Ranked)

Failed Step or Counter Flashing

Very Common

The metal flashing system around a skylight is engineered to shed water at each shingle course. Step flashing (L-shaped pieces woven between shingles) and counter flashing (overlapping the step flashing) must work together. Over 15-25 years, these components corrode, separate, or get sealed over with roofing tar that eventually cracks. Roofers cutting corners during re-roofing often damage or omit the proper flashing layers.

How to tell: Water appears at the upper (uphill) edge of the skylight. The leak occurs during rain but not in dry weather. Roofing tar or caulk is visible around the flashing (a sign of previous patch attempts). The skylight is 15+ years old.

Dried or Cracked Sealant Around Frame

Very Common

Skylights use butyl tape or silicone sealant between the frame and the roof deck. UV exposure and thermal cycling (the skylight glass heats to 150°F+ in summer and freezes in winter) degrades this sealant in 10-20 years. The frame separates microscopically from the curb, and water wicks through by capillary action.

How to tell: Water appears at the frame edges during rain. The sealant around the frame is visibly cracked or separated. The skylight is 10+ years old. Small amounts of water during light rain, larger amounts during heavy rain.

Condensation (Not a Leak)

Very Common

In cold weather, warm humid air inside the house hits the cold skylight glass and condenses. This drips onto the frame, the ceiling, and mimics a roof leak. It's especially common in kitchens, bathrooms, and homes with poor ventilation. A poorly insulated skylight frame worsens the problem.

How to tell: Water appears only in cold weather, not during rain. The skylight glass has visible moisture or frost on the inside surface. The problem is worse in humid rooms (kitchen, bathroom). There's no correlation with rain events.

Ice Dam Formation

Common

Heat loss through the roof melts snow, which refreezes at the eaves. The ice dam backs water up under the shingles and around the skylight. The skylight curb is especially vulnerable because it's a penetration that interrupts the water flow. Even well-flashed skylights can leak during ice dam events.

How to tell: Water appears during or after snow/ice events, not during rain. Ice is visible at the eaves or around the skylight. The roof has poor insulation or ventilation. The home is in a cold climate with freeze-thaw cycles.

Cracked Skylight Glass or Dome

Less Common

Acrylic dome skylights develop crazing and cracks from UV exposure after 15-20 years. Glass skylights rarely crack unless impacted by a branch, hail, or thermal shock. A cracked dome leaks at any rain angle and may leak from condensation running through the crack.

How to tell: Water enters through the glass area, not the frame. Visible crack, crazing, or discoloration on the glass or dome surface. The skylight is an older acrylic dome type. Water pattern follows the crack line.

How to Fix It

Reseal the Flashing and Frame

$50-150 DIY / $300-600 Pro

1Clean all old sealant from the flashing and frame junction.
2Apply a thick bead of roof-grade sealant (NovaBond or Geocel 2300) along the top and sides of the flashing.
3Do NOT seal the bottom (downhill) edge — water must be able to drain out.
4For step flashing: ensure each piece overlaps the one below by at least 2 inches.
5This is a roof repair — requires safe roof access. If the roof is steep, hire a roofer.

Replace Flashing Kit

$200-400 DIY / $500-1,200 Pro

1Skylight manufacturers sell replacement flashing kits specific to each skylight model and roof pitch.
2Velux, FAKRO, and Marvin all offer complete kits for $200-400.
3Installation requires removing surrounding shingles, installing the new flashing system, and reshingleing.
4This is the definitive fix if the existing flashing is corroded or improperly installed.

Replace the Skylight

$400-1,500 DIY / $1,000-3,000 Pro Installed

1If the frame, glass, or dome is damaged, replacement is the best option.
2Velux fixed skylights (most common) are $300-800 depending on size.
3Installation involves removing old skylight, inspecting and repairing the curb, installing new skylight with new flashing kit.
4Consider upgrading to a curb-mounted model (easier future replacement) or adding a solar-powered blind.

When to Call a Professional

Working on a roof near a skylight is especially dangerous — the skylight can break under your weight if you step on it.

Never seal the downhill (bottom) edge of skylight flashing — trapped water causes worse damage than the original leak.

If you see roofing tar around the skylight, it means someone has already tried to patch it — the underlying flashing likely needs replacement.

Ice dam leaks need the root cause fixed (insulation and ventilation) — patching won't prevent future events.

How to Prevent It

Inspect skylight flashing annually from the roof (or binoculars from the ground).

Keep gutters clear to prevent ice dams near skylights.

Ensure the attic has proper insulation (R-38 minimum) and ventilation to prevent ice dams and condensation.

Replace acrylic dome skylights proactively at 15-20 years before they crack.

Frequently Asked Questions

Condensation or leak — how do I tell?

Check the timing. Leak: during rain. Condensation: during cold weather without rain. Run your finger on the glass — if it's wet on the inside surface, it's condensation.

How long do skylights last?

Glass skylights: 20-30+ years. Acrylic domes: 15-20 years. Flashing: 15-25 years (often the first component to fail). The glass usually outlasts the flashing.

Should I replace or repair the flashing?

Repair (reseal) if: the flashing is intact but the sealant has failed. Replace if: the flashing is corroded, improperly installed, or has been patched multiple times.

Does a skylight leak void my roof warranty?

Usually not — skylights are separate from the roof system. But if a roofer damaged the flashing during re-roofing, that's a warranty claim against the roofer.