Skylights: The Flashing Is What Leaks, Not the Glass

Why sealant never holds

A skylight is a hole in your roof with a box around it. Keeping water out of that hole is a job for layered metal: pieces of flashing lapped so that water running down the roof is carried over the top of the skylight, around both sides, and back onto the shingles below it. Gravity does the work. No adhesive is involved.

Sealant is the opposite. It is a bead of flexible glue asked to hold out water by sticking to two surfaces that expand and contract at different rates, on a roof that swings 40 degrees between a February night and an August afternoon. In the Fraser Valley, silicone on a roof goes brittle in three to five years of freeze and thaw, then peels away from one side of the joint. From the ground it still looks sealed. It is not.

So when a skylight has been caulked, the leak has not been repaired. It has been postponed, and usually the water carried on running the whole time, just into the framing rather than onto the ceiling where you would see it.

What we actually find

• No step flashing up the sides. Somebody ran a continuous piece or a bead of sealant instead of individual pieces lapped with each shingle course. Water gets behind it at the first course.
• No head flashing or a head flashing lapped the wrong way, so water coming down the roof runs under the metal rather than over it. This one soaks the framing above the skylight and shows up as a stain a foot away from the glass.
• Ice and water shield missing around the curb. On a low slope or under a valley, the membrane around the opening is what saves you when water backs up. Plenty of skylights here were set with nothing but felt.
• A 20 year old unit with a failed seal. If the glass is fogged between the panes, that is the unit, not the flashing, and no amount of roof work fixes it.
• Condensation mistaken for a leak. A cold skylight in a wet bathroom with no fan will run with water down the inside of the frame. It looks exactly like a leak and there is nothing wrong with the roof.

We work out which of those it is before quoting anything, because the fix for each is completely different and three of them are not roofing.

One we did

A Chilliwack home got a full shingle re roof in September 2026 with two skylights set into the new field, which is the right time to do it: the flashing goes in with the roof rather than being cut into one that is already finished. The write up is here, with the photos.

How we install and reflash

We treat a skylight the way our trade taught us to treat a penetration in a pressure vessel: the detail is the whole job.

• Ice and water shield wrapped up the curb and out onto the deck on all four sides before any metal goes on.
• The manufacturer's own flashing kit where the unit has one. They are engineered for that curb height and that shingle thickness, and they cost less than the callback.
• Step flashing up both sides, one piece per shingle course, lapped so every piece sheds onto the one below.
• A proper head flashing at the top, taken up under the course above and out past both sides, so water is carried around the unit instead of into it.
• On a wide skylight or one close below a valley, a diverter above it, because a skylight sitting in the path of a valley is taking the water off half your roof.
• Sealant only where the manufacturer specifies it, as a secondary measure. Never as the thing holding water out.

Replacing an old unit

If the glass is fogged, the frame is cracked, or it is a plastic bubble from the seventies, the unit is the problem and reflashing a dying skylight is money wasted. Replacing it while the roof is open is the cheap moment to do it. Replacing it later means cutting back into a new roof.

That is worth thinking about now if a re-roof is coming. If your skylights are over fifteen years old, do them with the roof. It is a fraction of the cost compared to doing them separately, and it means the flashing and the shingles are the same age, installed by the same crew, in one warranty.

Deposit, timing and warranty

A single skylight is normally one day on site, weather permitting. We do not pad a one day job out to three.

On small jobs like a single skylight we take half up front, because the unit and the materials are most of the cost and they are bought before we start. The balance is due when you have walked it with us and you are happy.

Every job carries our 10 year labour warranty. The unit itself carries the manufacturer's own warranty, which is theirs, not ours, and we will show you what it actually covers rather than talk about lifetime anything.

One more thing, about leaks in general

Water shows up on a ceiling a long way from where it got in. It runs along the top of a rafter or the underside of the deck until it finds somewhere to drop. If a stain appeared near a skylight, the skylight is a reasonable suspect, but we have traced plenty of those to a chimney, a vent, or a valley three metres uphill. We find where it is actually coming from before we quote a repair, and we take photos so you can see it too.