Leak or Condensation?
Start here, because the fix is completely different.
Condensation forms when warm, moist indoor air hits a cold surface. NRCA notes that condensation on a skylight's interior face "may be misinterpreted as a leak." VELUX says homeowners often blame the skylight when the real cause is excess moisture in the room. Clues:
- It shows up on cold mornings, not after rain.
- It forms on the inside of the glass or frame.
- It's worse over kitchens and bathrooms.
A leak follows weather. Stains or drips after rain or snowmelt, water at the frame edges or the drywall around the opening, and stains that grow after storms point to the roof.
Fogging between panes is a third thing: the seal in an insulated glass unit has failed. VELUX describes clouding between the panes as a break in the inner seal. The unit doesn't leak water into the house, but the seal can't be restored.
Why Skylights Leak
Flashing and installation. The Department of Energy recommends mounting skylights above the roof surface on a curb, with flashing and waterproofing over the flanges, because improperly installed skylights commonly leak. Flashing that's been patched with sealant, bent or never integrated with the roofing is the usual suspect.
Curb height on flat and low-slope roofs. The 2021 IRC, adopted in New Mexico without changes to this section, says skylights on roofs with less than a 3:12 pitch must be mounted on a curb at least 4 inches above the roof, unless the manufacturer's instructions specify otherwise (R308.6.8). NRCA goes further for low-slope roofs, recommending curbs tall enough for an 8-inch base flashing height. On older Albuquerque flat roofs, skylights set nearly flush with the roof, or buried as the roof was built up over the years, are common leak points.
Aging plastic domes. Many older flat roofs here have acrylic "bubble" skylights. The DOE notes plastic glazing scratches easily and may become brittle and discolored over time. A dome that's cloudy, yellowed or cracked is near the end of its life.
Failed seals. VELUX notes that leaks typically point to an issue with the window sealant, and that discoloration can be a sign moisture is getting through.
A reroof without new flashing. A VELUX contractor article notes that during a reroof the skylight gets jostled, which "more often than not leads to leaking" if it isn't reflashed.
On a flat roof, water often travels before it shows. A stain near a skylight can come from the skylight, from a nearby penetration, or from ponding water against the curb. Our guide to flat roof drainage explains why standing water at a curb matters.
Reflash, Repair or Replace?
Reflash when:
- The skylight itself is sound: no fogging, cracks or brittle plastic.
- The leak is at the flashing or curb.
- The curb is tall enough to flash properly.
Replace when:
- The glass is fogged between panes or the plastic dome is brittle, cloudy or cracked.
- The curb is too low and needs rebuilding anyway.
- You're reroofing. VELUX recommends replacing skylights when you replace your roof, because the old flashing comes off anyway and doing both together keeps the roof and skylight warranties in sync.
- The skylight is old. VELUX says many of its skylights last 20 years or more and suggests upgrading after about 30.
Avoid: caulking over the flashing or the dome edge as a permanent fix. It hides the problem for a season.
Skylights and a Reroof
If a reroof is coming, plan the skylights with it. The flashing around a skylight is part of the roof system, and manufacturers specify flashing kits for each roof pitch and material. VELUX's warranty, for example, excludes leaks from reroofing without the manufacturer's underlayment and approved flashing. On a flat roof, the reroof is also the time to raise a low curb.
New Mexico's state permit rule (14.5.2.8 NMAC) requires a permit for all re-roofs and doesn't list skylight work as exempt. Inside Albuquerque or unincorporated Bernalillo County, check with that building department. See roof permits in Albuquerque.
Should You Keep the Skylight at All?
Skylights bring in light, and in New Mexico they also bring in heat. Our guide to skylights and ventilation in a desert climate covers the tradeoffs. If you're removing a skylight, the opening is framed in and roofed over like any other opening. The process is similar to closing a swamp cooler opening.
Timberwolf repairs, reflashes and replaces skylights as part of roof repair and roof replacement. A Free Roof Report includes the flashing and curb around each one.

