How to Maintain Commercial Skylights to Prevent Water Intrusion

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The fastest way a small skylight problem turns into a pricey repair is simple: nobody looks at it until water is already dripping onto the floor below. Skylights rarely leak because the glazing itself fails. They leak because the curb around them does: sealant that has cracked and pulled away, counterflashing that has worked loose, or a drain that nobody cleared before the leaves piled up.

Why commercial skylight maintenance can’t wait

A leaking skylight rarely announces itself where the leak actually starts. Water follows the path of least resistance along framing members, insulation, and vapor barriers before it finally shows up as a stain on a ceiling tile, sometimes ten or fifteen feet from the curb itself. By the time anyone notices, wet insulation and a soaked deck have usually been sitting there for weeks.

That lag is exactly why a scheduled walk beats a reactive one. Catching a cracked sealant joint in September is going to be a lot better than in February, after a winter of freeze thaw cycling has widened the gap, tends to mean a wet ceiling, a business interruption, and a much bigger invoice. If you need professional help to fix or replace your leaky skylight, contact us today and we’ll be able to fix your issues ASAP! 

Step 1: Start the inspection from inside

Before anyone gets on the roof, walk the building underneath every skylight. Look at the ceiling tiles, drywall, or exposed deck directly below each unit for staining, discoloration, or a soft spot. A ring shaped water stain almost always means an active or recent leak.

This step takes ten minutes and tells you exactly which skylights need the closest look. It’s also the easiest thing to skip when a facilities team is busy, which is exactly why it gets skipped, and why leaks get found late.

Step 2: Check the curb flashing and sealant

The curb, the raised frame the skylight sits on, is where almost every leak actually starts. Walk the perimeter of each unit and look for sealant that has gone chalky, cracked, or separated from either the curb or the skylight frame. Check that the counterflashing, the metal trim that laps over the membrane, is still snug and not loose.

Flashing is consistently identified as one of the most failure prone details on a low slope roof. The National Roofing Contractors Association’s guidance on roof flashing treats it as its own category of inspection for exactly this reason: it is a joint between two different materials, and joints move differently than the field of the roof around them.

Step 3: Clear the drainage path around every curb

Water that cannot drain away from a skylight curb has more time to find a way in. Clear leaves, granules, and any debris that has built up against the low side of the curb, and confirm the nearest roof drain or scupper is not blocked.

This is also the moment to look for ponding that sits well past the point where the roof should have drained. Standing water against a curb means that seal is under more pressure than it should be, for longer than it should be.

Step 4: Watch for movement from thermal cycling

Roof membranes and metal flashing expand and contract with temperature, and a skylight curb sits at the exact spot where several materials with different expansion rates all meet.That movement can make a sealant joint loose or pull counterflashing away from the fastener line, wearing down over time.

Look for hairline gaps, fasteners that have started to back out of the counterflashing, or a joint that looks slightly different from the same joint on another skylight about the same age. Do not touch loose components. Restrict roof access and arrange prompt professional assessment.

Step 5: Build spring and fall walks into the schedule

Two inspections a year catches most of what matters. A spring walk tends to find whatever winter movement opened up. A fall walk confirms drains and curb bases are clear before snow and ice load the roof for months.

Both visits are also a chance to compare current photos against the last set. A joint that looked fine in the fall and looks different in the spring tells you something a single inspection never can: that something changed, and roughly when.

Step 6: Keep a written record, not a memory

A photo, a date, and a one line note for each skylight is enough. Six months from now someone can look at a joint and know if it looks the same, better, or worse than it did last time.

This habit pays off twice. It catches slow moving problems that a single visit would never see, and it gives a roofing contractor a head start.

Common mistakes that undo good maintenance

The most common mistake is not skipping maintenance entirely. It is doing a rooftop walk without ever checking underneath the skylights first, which means small leaks get missed until they show up somewhere else. The second most common mistake is treating a sealant touch up as a permanent fix rather than a stopgap, when the real issue is a flashing detail that needs to be redone properly.

A close third: assuming every skylight on a roof ages at the same rate. Orientation, shade, drainage, and foot traffic all differ from unit to unit, even on the same building. Two skylights installed on the same day can be in noticeably different condition five years later.

When it’s time to call a roofing contractor

Only authorized, trained personnel using appropriate fall-protection measures should access or inspect the roof. Facilities staff may perform the interior inspection from floor level. Sealant replacement, flashing repair, and curb re-detailing are a different category of work, and they are worth handing to a roofing contractor who does this daily, both for the workmanship and for the fall protection the job requires.

Frequently asked questions

Skylight and flat roof maintenance across Southern Ontario

Industrial Roofing Services Limited maintains, repairs, and inspects skylights and flat roof systems for commercial and institutional buildings throughout the GTA and Southern Ontario. If it has been more than six months since anyone looked at your skylights from either side of the roof, get in touch with our team and we will build a maintenance visit around your building’s specific roof.

The post How to Maintain Commercial Skylights to Prevent Water Intrusion appeared first on Industrial Roofing.

Most commercial roof problems are visible before they become expensive. The trouble is that most property managers don’t know what they’re looking at when they’re up there, so small deficiencies compound quietly until someone calls about water coming through a ceiling tile.

This checklist gives you a structured way to walk a commercial flat roof and document what you find. You need good eyes, a phone camera, and the discipline to do it twice a year.

If you prefer to have a professional handle inspections, our professional flat roof assessment team can provide a written condition report with repair priorities and estimated remaining life, which most institutional landlords and property insurers now expect.

Before you go up: safety and access requirements

Ontario requires fall protection when working within 2 metres of an unprotected roof edge. If your building has guardrails or a permanent fall arrest anchor system installed, confirm they’re rated and in good condition before putting weight on them.

If your rooftop does not have compliant edge protection, you should not be up there without a proper harness and an anchor point rated for the activity. Our rooftop safety system installation team installs permanent guardrail and anchor systems that make routine roof access safe and code-compliant.

At minimum before any roof walk: check weather (don’t walk a wet membrane), tell someone you’re going up, wear soft-soled shoes, and bring your phone for documentation.

Membrane surface inspection

Walk the full surface area in a grid pattern rather than wandering. You’ll miss things if you don’t systematically cover the roof.

Blistering. A small blister under 6 inches in diameter that feels firm is usually a cosmetic concern. A large blister or one that feels soft and spongy when you press it means there’s moisture or air trapped in the assembly beneath. Mark it for professional evaluation.

Cracks and splits. Any visible crack in the membrane surface is a potential water entry point. Particularly watch the perimeter area within 2 feet of parapet walls, where thermal movement stress concentrates.

Open or lifted seams. Run your hand along seams. On TPO and PVC, seams should be solid and fused. Any seam you can get a fingernail under is a problem.

Granule loss on modified bitumen. Patchy areas where the granule surface has worn off expose the underlying asphalt to UV. Widespread granule loss is a sign of accelerated aging.

Surface debris and ponding water. Standing water 48 or more hours after rain is a drainage problem. Check if drains are clogged. Debris mounds trap moisture against the membrane.

Drainage system check

Every drain, scupper, and overflow drain on the roof needs to be clear.

Roof drains: remove the strainer and check the drain body for debris. Pour a bucket of water slowly and confirm it drains at a reasonable rate rather than backing up.

Scuppers: look through them from the roof side. Any bird nesting material, leaves, or debris blocking a scupper is a potential ponding problem during heavy rain. Ontario had several significant late-summer rain events in 2024 and 2025 where blocked scuppers caused interior flooding that proper drainage would have prevented.

Overflow drains: these emergency relief drains are set higher than primary drains. If they show signs of consistent flow (rust staining, debris rings), your primary drains aren’t doing their job.

Flashings and terminations

Flashings are the strips of material that transition from the membrane surface up and over any vertical element: parapet walls, expansion joints, curbs. They’re the most common failure point on commercial roofs.

Base flashings. At every parapet wall, the membrane should turn up the wall face a minimum of 8 inches. The termination bar at the top should be firmly anchored, with sealant at the top edge intact. If the sealant is cracked or the termination bar is pulling away, water can get behind the flashing.

Expansion joints. These should have a continuous flexible bellows or cover above them. Any cracking or splitting in an expansion joint cover needs professional repair because the joint is designed to move, and a rigid repair won’t last.

Penetrations and equipment curbs

Every penetration through the membrane is a potential failure point. On older commercial buildings, penetrations accumulate over years of tenant improvements and HVAC upgrades, sometimes with no formal flashing at all.

For each penetration, check is there a proper curb? Is the flashing continuous and in contact with the curb sides? Is sealant at the top of the curb flashing intact and not cracked? For conduit, is the entry point sealed?

Pay particular attention to areas where multiple penetrations cluster together, typically around HVAC units. Crowded penetration areas are hard to flash properly and often have overlapping repair history that creates complex water paths.

Rooftop equipment condition

You’re not doing an HVAC inspection. But the condition of rooftop equipment affects your roof.

Condensate discharge: HVAC condensate should discharge through a proper line to a drain. If condensate is draining directly onto the membrane, it concentrates water in one spot and can contain refrigerant oil that degrades some membrane types over time.

Unit mounting: check that equipment legs are sitting on proper curbs or isolation pads, not directly on the membrane. Equipment resting directly on the membrane creates abrasion and puncture risk during servicing.

Parapet walls and coping

Parapet walls are the short walls around the perimeter of most commercial flat roofs. They take significant weather exposure and are a common source of leaks that appear to come from the roof but actually enter through the wall.

Coping: the metal cap on top of the parapet should be continuously seamed with no open joints. Water that enters through a coping joint runs down inside the wall cavity and can exit at ceiling level inside the building, nowhere near the roof perimeter. Property managers frequently assume the roof is leaking when the actual failure is coping.

Mortar joints: on masonry parapet walls, check mortar joints for deterioration. Spalling brick or eroded mortar is a water infiltration path that has nothing to do with the roof membrane.

Documentation: what to photograph and record

After every roof walk, document what you found. A photo log that goes nowhere is useless. For each deficiency, take a wide-angle photo showing location relative to a fixed reference, take a close-up of the defect, and write a brief description of what it is and approximate size.

Keep this documentation in a folder per building, organized by inspection date. When you’re negotiating a capital repair budget or making a warranty claim with the membrane manufacturer, this record is what gets decisions made quickly.

When to call a professional

Do the semi-annual walk yourself. Call a professional when you find a blister larger than 12 inches, there is standing water that hasn’t drained within 48 hours of the last rain, a seam has opened, you find any deficiency you can’t clearly categorize, the roof is over 15 years old without a recent condition assessment, or you’re buying, selling, or refinancing the building.

A professional flat roof inspection includes non-destructive testing, documented condition ratings, and repair prioritization. If you suspect wet insulation, add infrared scanning to the scope. An infrared scan after a clear day will show thermal anomalies where wet insulation retains heat differently from dry areas.

Printable commercial roof inspection checklist Download PDF

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