Skylights add daylight and lift a room’s mood, but they also puncture the most critical barrier your home has against water. When a skylight leaks, the damage rarely stays local. Moisture migrates along rafters, saturates insulation, stains ceilings, elevates humidity, and, if ignored, rots the deck or framing. The good news is that most skylight leaks have predictable causes. With correct detailing and disciplined maintenance, you can keep the view of the sky without inviting the weather in.
I have walked hundreds of roofs where the skylight told the story. Sometimes the fix was a simple bead of compatible sealant along a corner where a homeowner had accidentally dislodged a shingle. Other times, the “skylight leak” was a symptom of larger roof failure, and the right solution was a full roof replacement. The difference lies in diagnosis and technique. This guide lays out the practical approach, the mistakes that trigger leaks, and how to decide between targeted skylight repair and broader roofing repair.
How skylights are supposed to keep water out
A skylight system is part window, part roof penetration. If it is installed according to manufacturer instructions, three lines of defense work together.
First, the glazing and frame shed water from above. Fixed units are sealed at the factory, vented units rely on weatherstripping around operable sashes. Second, the flashing kit, typically specific to the skylight brand and roof pitch, steps and counter-steps water around the opening. Think of this as a miniature version of how a chimney flashing is woven into shingles. Third, the underlayment seals the roof deck itself. High-quality self-adhered membranes form a watertight bond around the skylight curb or frame, so even if wind-driven rain gets past shingles and flashing, it cannot reach the wood.
When any one of these three layers is skipped, substituted, or installed out of order, leaks find their way in. That is why a small patch often fails, and why a roof repair specialist will begin with a methodical inspection rather than a caulk gun.
Where leaks really come from
After years of seeing the same patterns, I look for five common sources. The first is improper flashing. A skylight set into shingles without a true step flashing kit, or with site-bent metal that does not match the roof pitch, will likely leak during wind-driven rain. The second is aging seals. On vented units, weatherstripping compresses and cracks. On older acrylic domes, the curb-to-frame gasket loses elasticity, and the weep holes clog with debris.
The third source is underlayment failure at the curb. If a skylight sits on a curb without a continuous strip of self-adhered membrane wrapping up the curb and out onto the deck, water that gets under shingles can ride the deck and enter at the fasteners. Fourth, poor integration with roof features. Skylights placed just upslope of a valley or below a tall wall need diverters, crickets, or extended flashing. Otherwise, they are constantly bathing in concentrated water flow that overwhelms the system. Lastly, condensation masquerading as leaks. In cooler climates or homes with high interior humidity, warm moist air reaches a cold skylight and condenses. The drip lands on drywall and looks like a leak, but the fix is ventilation, insulation, or a skylight upgrade with low-E glazing, not caulk.
The key is to verify which failure mode you have. A flashlight and a garden hose are still a roofer’s best tools. I isolate the test: spray the upslope shingles well above the skylight, then the sides, then the head flashing, watching from inside the attic when possible. If nothing shows until you soak the sash itself, you are dealing with glazing or weatherstripping. If water appears when the upslope shingles are sprayed, look to underlayment and head flashing.
Repair, restoration, or replacement
Not every leak demands a new skylight, and not every skylight repair brings the roof back to health. The right choice depends on age, extent of damage, and the roof’s remaining life.
Skylights older than 20 years usually do not justify a major repair. Even if you stop today’s leak, worn seals and outdated glazing will likely trigger a new issue soon. In that case, plan to replace the unit when you tackle home roof replacement. Modern skylights with laminated or tempered low-E glass, thermally broken frames, and factory flashing kits perform better, last longer, and resist condensation.
If the roof is nearing the end of its life, try not to invest heavily in an isolated skylight fix. You might pay twice, once for an emergency repair, then again for a reflash during roofing replacement. I often recommend a strategic approach: stabilize the leak with a temporary measure, then coordinate skylight replacement with the full roof replacement. Roofing companies Los Angeles property owners trust, for example, often bundle skylight upgrades with tile roof replacement or asphalt shingle reroofs to ensure everything is integrated under new underlayment.
If the roof is healthy and the skylight is under 10 to 15 years old, a targeted skylight repair makes sense. That might include replacing the flashing kit, re-wrapping the curb in new self-adhered membrane, cleaning weep holes, and updating weatherstripping. When handled by a licensed roofing contractor who follows manufacturer specs, this kind of repair should last the remaining life of the roof.
Anatomy of a proper skylight repair
The best roofing repair contractors follow a sequence that respects water’s path. Start by removing shingles around the skylight to expose the existing flashing. Do not pry blindly on the frame. On most standard deck-mounted skylights, you will find a head flashing, step flashing along the sides, and a sill flashing. If any piece is site-fabricated, corroded, or misaligned, plan to replace with the factory kit that matches the skylight model and roof pitch.
The deck is next. Inspect for rot around the opening, especially at the downslope corners where water will concentrate if the sill flashing failed. A half-inch of soft plywood may feel like it can be “bridged” with new shingles. Do not do it. Cut back to solid wood and replace the damaged area with matching thickness sheathing, fastened to actual support. If rot has crept into rafters or the curb, rebuild as needed. Compromised framing telegraphs movement to the flashing, which reopens the leak.
Once the structure is sound, apply underlayment. I prefer a high-quality self-adhered membrane that remains flexible in heat and cold, installed first on the downslope, then overlapping up the sides, then over the head. Wrap each piece up the curb by a few inches and out onto the deck. The goal is a continuous, shingle-styled layering that forces water to the exterior. Pay attention to the corners, where a simple back-cut and fold can create a tight seal without bunching. Do not puncture the membrane near the curb with unnecessary fasteners.
Now install the flashing kit, starting at the sill. Each step flashing piece should interleave with each shingle course. On roofs with thicker profiles like some laminated shingles, ensure that the flashing sits flat and is not bridged, or it will kink and open gaps later. Use only fastener locations the manufacturer specifies, and never drive screws through exposed horizontal surfaces of the flashing where water will collect.
Finally, reset shingles or replace with new if the old ones were brittle. Match color and weight as closely as you can. On the upslope side, consider a small diverter cricket if the roof plane feeds heavy water directly at the head. In snow country, ice and water shield extending well above the head flashing reduces ice dam risk.
For venting units, check the weatherstripping and the operator. If the sash does not close with uniform compression, no amount of exterior work will stop wind-blown rain. Many manufacturers sell replacement gaskets. Clean the weep channels along the frame so that condensation and incidental water can drain.
Why caulk is not a strategy
Every roof repair service tech I respect carries sealant. The difference is when they use it. Sealant is a backup, not the primary defense. Slathering roofing cement along exposed edges of a skylight provides a brief reprieve, then shrinks or cracks, trapping water where it cannot dry. I have seen more damage caused by improper gooping than by the original leak.
There are exceptions. A compatible high-performance sealant can bridge a hairline crack in a corner flashing as a short-term fix. It can bed a flashing leg against a slightly irregular shingle to stop capillary draw. It can seal the heads of necessary fasteners. But it should not substitute for a missing step flashing or a botched underlayment.
If a roofer proposes to “seal the skylight” without removing shingles, ask questions. Often the honest answer is that they are buying you time until a scheduled roofing replacement or until weather permits a proper repair. That is fine if everyone understands the limits.
Distinguishing roof leaks from skylight condensation
Homeowners sometimes point to drips on the inside of the acrylic dome and assume the skylight failed. In many homes, especially after a new tight roof and windows go in, indoor humidity climbs. Hot showers, cooking, or unvented gas heaters add moisture. If the skylight has single-pane acrylic or older double glazing with failed seals, the interior surface gets cold. Water forms, runs down, and soaks the drywall.
The fix here is not flashing. Improve ventilation with bath fans that actually vent outside, not into the attic. Add air sealing and insulation around the skylight shaft. If the skylight is old, upgrade to a modern unit with insulated, low-E glass and a thermally broken frame. The difference is dramatic. In a winter service call I handled a few years ago, a family thought their new roof was defective because the skylight was “leaking” on frosty mornings. A hygrometer showed 55 percent RH in the living room. After adding a continuous bath fan set to 30 CFM and swapping the skylight for a laminated low-E unit, the drips stopped.
How roof age and system type affect skylight detailing
The roof material alters the flashing strategy. On asphalt shingle roofs, factory flashing kits are reliable when installed precisely. On tile roofs, it is a different game. The tile stands off the deck, and water flows beneath as well as over. A proper tile skylight install requires a raised curb, pan flashing with side channels, and waterproofing over the deck. A tile roof replacement is the right time to set the curb height and pan flashing to match the tile profile. Improvised flat-roof flashings under tile often fail within a season.
On low-slope roofs, skylights should be curb-mounted, not deck-mounted, and the membrane roofing must be integrated with the curb flashing. For single-ply membranes like TPO or PVC, the membrane turns up and over the curb, often with a preformed corner. For built-up roofs or modified bitumen, multiple plies wrap the curb. Ponding is the enemy. If a skylight sits in a depression, water will live on the flashing and find a path. In commercial roof maintenance, I recommend building small saddles to direct water away from skylights when the roof is re-coated or restored.
If your roof uses a coating system, confirm that the coating is compatible with the skylight frame and flashing metals. Incompatible solvents can attack gaskets or embrittle acrylic domes. Reputable roof coating services understand when to mask skylight frames, when to roofing inspection services coat up to but not over certain flashings, and how to maintain weep paths.
When a leak signals bigger roof trouble
Some skylight leaks are actually a pressure relief valve for a failing roof. If you see shingle granules in gutters, widespread curling, brittle tabs, or multiple active leaks, focus on the system, not the symptom. A residential roof replacement will address chronic water entry points, and new underlayment will improve skylight resilience. In older homes where felt underlayment was used, migrating water could ride the deck until it found the path of least resistance at the skylight opening. Under modern standards, an ice and water barrier around penetrations creates a reliable secondary seal.
Tile roofs raise a different issue. Underlayment beneath tile is the true waterproofing. If it has aged out, replacing individual flashings around a skylight may not stop leaks for long. Tile roof replacement or a targeted underlayment replacement around the area might be the only responsible fix. Skilled roofing repair contractors can sometimes extend life with localized underlayment replacement and re-laying tile, but the work must be careful to avoid broken tiles and mismatched planes.
On flat commercial roofs where skylights are part of a daylighting strategy, a leak can point to aging seams, saturated insulation, or past coating layers that have cracked. In that case, roof restoration or sectional replacement combined with re-flashing skylight curbs provides a more durable outcome than chasing a drip.
Working with the right contractor
Skylight work straddles roofing and fenestration. The best results come from licensed roofing contractors who are fluent in both. Ask if they are factory-certified for the skylight brand you own or plan to install. That matters, because flashing kits and installation details vary by model. A competent roof installation contractor will show you how the factory pieces integrate and will not improvise unless the manufacturer provides for it.
Locally, roofing companies Los Angeles homeowners rely on have an added challenge. Heat, UV, and Santa Ana winds punish sealants and make debris-driven wear worse. On these roofs, I look for contractors who specify underlayments and flashing metals that hold up under thermal cycling. In coastal zones, galvanic compatibility and corrosion resistance are vital. Aluminum frame touching copper flashing with salty air is a recipe for galvanic corrosion and failure.
If you already have a favorite roof repair service, ask them to document the fix. Good roof repair services leave photos of each stage, especially of underlayment and flashing before shingles go back. That documentation builds trust and helps if a future issue arises. The best roofing company for your home is the one that treats a skylight as part of a system and is frank about what is a durable repair versus a short-term patch.
Preventive maintenance that actually matters
A little attention each season can add years to a skylight’s life and prevent preventable leaks. Clear debris. Leaves, needles, or granules that pile against the upslope side of a skylight hold moisture and create capillary action up and under flashing. Keep gutters clear so water does not back up on the roof plane where the skylight sits. From inside, check drywall corners around the light shaft for hairline stains after heavy storms. Early signs are cheaper to fix.
Operate vented skylights a few times a year to keep mechanisms moving and to check weatherstripping compression. If you see daylight where you should not, address it before the rainy season. On low-slope commercial roofs, inspect the seams around skylight curbs whenever you schedule maintenance. Commercial roof maintenance programs that document moisture scans can catch saturated insulation near skylights, a sign that the flashing or membrane has lost integrity.
Finally, do not paint or coat over weep holes, frame joints, or gaskets. That short-circuits the drainage paths the skylight relies on. I once traced a stubborn “leak” to a beautiful but ill-advised interior repaint where the painter sealed the skylight’s interior drainage channel. The fix required stripping paint from the channel and fitting new interior trim, not any roof work at all.
Costs, timelines, and setting expectations
Owners want to know what to expect, and the honest answer is that skylight work spans a range. A straightforward reflash on an asphalt shingle roof with a healthy deck can often be done in half a day for labor plus materials, with costs varying by region. Add time if the unit is large, steep roof access is challenging, or matching shingles requires a supply run. Replacing a modern skylight with a same-size unit typically takes a day, including interior trim touch-up and exterior flashing. If the roof deck is compromised or the light shaft has to be rebuilt due to mold or rot, plan on two days and add budget for carpentry.
During a full roof replacement, adding or replacing skylights is the most efficient. The roof is open, underlayment is fresh, and integration is cleaner. If you are already investing in a home roof replacement, it is smart to retire any skylights older than 15 years and upgrade to current models. That way, the new system ages together, and you avoid reopening the roof later.
If you manage a commercial property, coordinate skylight work with roof restoration or coating cycles. Many coatings need dry, clean surfaces and specific curing windows. A roofing repair contractor who understands the coating’s chemistry will stage skylight re-flashing ahead of the coating application so the membrane ties are primed and fully cured before the topcoat.
When to walk away from a repair
Sometimes the best advice is to stop investing in a failing approach. If a skylight leaks due to inherent design flaws, such as old curb-less acrylic domes on low-slope roofs, or if the opening sits in a valley where water constantly overwhelms the flashing, it is kinder to your budget to redesign. That might mean raising the curb, relocating the opening during roofing replacement, or switching to a tubular daylighting device with a smaller footprint in a problem area. I have removed more than one chronically leaking unit and replaced the opening with a well-insulated roof section, then added a new skylight in a better location.
For heavy snow regions, I advise avoiding wide skylights low on the roof where snow loads shear against the head flashing. If you must have them, design crickets and use enhanced ice barriers. Conversely, in hot climates, prioritize glazing that reduces solar heat gain or add exterior shades. Overheating can drive indoor humidity changes that contribute to condensation and the perception of leaks.
A brief homeowner checklist for leak-free skylights
- Verify that your skylight has the correct factory flashing kit for your roofing type and pitch, not site-bent metal. Confirm that a self-adhered membrane wraps the curb and laps onto the deck under the shingles or membrane. Keep the upslope area clear of debris, and ensure gutters drain freely so water does not pond around the opening. For vented units, inspect and replace weatherstripping if compression is uneven, and keep weep holes open. If your roof is within 3 to 5 years of replacement, coordinate skylight upgrades with the full roof replacement to avoid duplicated labor.
Final perspective from the roof
There is a satisfying moment at the end of a good skylight repair. The roof plane lies flat and clean, flashing sits tight with the shingles, and water streams exactly where it should. Inside, the shaft glows without the sour smell of damp drywall. That result does not come from secret products. It comes from respect for how roofs shed water, patience with sequencing, and a willingness to say no to band-aids when they do not make sense.
Whether you are calling a roof repair specialist for a drip above the stair or planning a larger roofing replacement, treat the skylight as part of the system, not an accessory. Choose a licensed roofing contractor who will show you the layers, explain the trade-offs, and match the solution to the roof’s stage of life. Do that, and your skylight will bring the sky in, not the rain.