Skylights are popular architectural elements that let natural light into an otherwise darkened room. So, if anything should pour in through your skylight, it should be golden sunshine, not rainwater. If your skylight leaks, don’t wait to fix it. A small leak could indicate water collecting around the skylight, which could rot the roof decking.

Maryland general contractor Alan Hill warns that while major skylight repair jobs aren’t DIY-friendly, homeowners can find and seal most leaks with the right equipment.
Hill adds that the problem may not even be a leak — it could be condensation. And if it is a leak, it may not be coming from the skylight itself, but from another part of the roof. Roof leaks tend to be insidious that way.

Here, we explore the causes of skylight leaks, how to repair a leaking skylight on your own and tips for preventing future leaks through proper maintenance.

  • Note: Roof work is dangerous, so follow recommended safety guidelines for setting up and working from your ladder. Always use proper safety equipment, including non-slip shoes and a roof safety harness. If the roof is too steep to walk on comfortably or you have concerns at all, hire a pro.

Common Causes of Skylight Leak

When you see water dripping from your skylight, put something under the drip to catch the water. Then try to determine where the drip originates. You’ll probably need a stepladder for a close-up view from indoors.. Here’s what to look out for when fixing skylight leaks:

Condensation buildup

While you’re examining the skylight,  look for signs of condensation on the glass. What looks like a leak is sometimes condensation buildup on the skylight glass, especially in humid environments. Poor ventilation can cause water to drip from the skylight frame, mimicking a leak. If you find any, you’ll probably notice it collects at certain points and drips from there.

The Fix:

  • The best remedy for condensation is ventilation, so open the skylight if it’s operable.
  • If the skylight doesn’t open, consider using a fan to improve air circulation.
  • Hill also recommends going on the roof and clearing obstructions from the weep holes, the tiny holes on the lower part of the skylight frame that allow condensation to drain. This will prevent the skylight glass from clouding up.

Faulty skylight

If the skylight opens, check the rubber gasket around the frame for signs of deterioration or mold. That would indicate the skylight isn’t sealing all the way, and moisture is dripping between the window casing and the frame.

The Fix:

  • Replace the gasket if it shows signs of wear or damage.
  • Remove any bits of debris preventing the skylight from closing all the way.
  • Your inspection may reveal moisture around a cracked section of the skylight. Although it may be possible to remove and repair the cracked part, in most cases, you’ll have to replace the entire skylight.

Cracked skylight pane

Cracks in a skylight pane can develop from hail, falling branches or long-term exposure to UV rays that weaken the material over time. Even a hairline crack can expand with temperature fluctuation, allowing water infiltration.

The Fix:

  • As a short-term fix for minor damage, you can apply a temporary patch using waterproof tape or a specialized sealant.
  • A full skylight replacement is recommended for a permanent solution, especially with older units, to ensure a watertight seal.

Faulty roof flashing

Once you’ve eliminated condensation and skylight defects, any water you see must be coming through the roof. It’s either seeping under the flashing or getting through the seal between the flashing and the skylight.

If it’s coming from the frame on the upper part of the roof slope, that’s easier to diagnose and repair than if it’s coming from the lower part of the frame. Water tends to travel along the roof decking, so a leak from the lower part could originate from anywhere on the roof. One from the upper part is almost always from the skylight flashing.

How to Seal and Fix a Skylight Leak Yourself

Reseal the flashing

If you determine the water is coming from the flashing, the next step is to go on the roof with a caulk gun and the appropriate sealant. Hill recommends a sealant designed specifically for roof flashing, such as Loctite Roof & Flashing Sealant. Butyl and silicone sealants are not recommended for this project.

The damage may be easy to spot. You may find parts of the existing sealant have chipped or crumbled away from exposed flashing. In that case, scrape off all the loose bits with a putty knife and apply a bead of new sealant to the exposed area.

To examine the parts of the flashing that sit flush against the roof, you’ll need to peel back the shingles. Apply the sealant generously to the edges of the flashing, especially along the head of the skylight on the upper part of the roof. Remember that any water seeping under the flashing at the top of the skylight can trickle down and drip from a lower part.

When to reinstall the flashing

Quality skylights come with flashing, which Hill says is leakproof when installed correctly. Without knowing it, however, a DIY or inexperienced pro installer could damage the flashing by nailing it to the roof, which Hill says you should never do.

If you find nails, deteriorated or rusting flashing or gaps in the step flashing along the sides of the skylight frame where shingles and flashing are layered, it’s probably best to rip up the shingles and redo the flashing.

If things reach this point, Hill recommends hiring a vetted contractor. That way you’ll be sure the proper flashing is used and installed correctly.

  • Note: It’s an extra expense, but it’s better than doing the job yourself and discovering the skylight still leaks.

Materials you’ll need for skylight repairs

  • A caulk gun for precise sealant application
  • Roof flashing sealant like Loctite (avoid silicone or butyl-based products)
  • Putty knife to remove old sealant and debris
  • Safety equipment, including a roof harness and non-slip footwear

Preventing skylight leaks with proper maintenance

  • Once a year, especially before the rainy season sets in, inspect the skylight, flashing and caulking thoroughly and look for areas of stress
  • Regularly clean the roof and skylight and keep them free of leaves, moss and other debris
  • Ensure proper attic ventilation to reduce condensation
  • Reapply sealant if you notice any cracks on the skylight or if it begins to pull away from the frame

FAQs

Can you seal a skylight from the inside?

Sealing a skylight from the inside may be ineffective. Most skylight leaks originate from outside elements like faulty flashing, deteriorated gasket or debris collection, so repairs typically need to happen on the roof.

How much does it cost to repair a skylight leak?

For minor DIY repairs, the cost can be as little as $20–$50 in materials. If the extent of the work warrants a professional, the average cost of repairs could be approximately $350 and could go up to $1,000, depending on the issue and location.

About the Expert

  • Alan Hill is a licensed general contractor based in Maryland with years of experience in roofing and skylight installations. Hill specializes in leak detection, roof flashing installation and home weatherproofing.

Sources

Author
Chris Deziel
Chris Deziel is a freelance service journalist who worked in landscaping and home improvement for more than thirty years. He has published over 10,000 how-to and expository pieces on home improvement and nature topics since he began writing in 2010. Deziel lives and works in an off-grid home in California where he enjoys recording original music an...
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Chris Deziel