A skylight leak gets blamed on the glass because that is the part you can see from the floor. Water usually enters at the joint between the unit and the roof: the curb, the step flashing, the underlayment around the opening, or a clogged weep that can no longer drain the frame. Replacing the pane and leaving a tired curb is how people buy the same stain twice.
How to tell the paths apart
Glass and gasket leaks often show up on the frame itself, or as condensation between panes on a sealed unit that has lost its seal. Condensation inside a double pane is a unit problem. It is annoying and it is not a roof leak. Water that stains the drywall beside the shaft, especially during wind-driven rain, is much more often flashing or a gap where the roofing meets the curb.
From the attic, look at the wood around the opening. Darkened rafters on the uphill side suggest water getting under the flashing above the unit. Staining only at the bottom of the shaft can be a weep or an interior condensation drip. Those want different repairs.
What a proper repair includes
A lasting fix usually means lifting shingles around the skylight, replacing step and head flashing, and tying new underlayment onto the curb. On a curb-mounted unit, the curb itself may be soft. A deck-mounted unit depends even more on the flashing kit made for that model. Mixing a universal flashing kit with a frame it was not drawn for is a leak with new metal.
If the roof is near the end of its life, doing the skylight in isolation can mean paying to disturb shingles that will be torn off in a year. If you are already planning a replacement, replace or reflash the skylight in the same scope so the new field and the new curb are one system.
Maintenance that prevents the repeat
Debris on the uphill side of a skylight dams water against the head flashing. Valleys that end near a unit do the same. Keep that area clear, from the ground or by someone who is equipped to be on the roof. Do not caulk the weeping slots on the frame shut. They exist so the frame can drain. Sealing them “because water was there” traps the next rain.
Questions readers ask
Should I replace the skylight when I reroof?
If the unit is old enough that the gasket is cracked, the seal has failed, or the flashing kit is no longer made, yes. A new roof around a twenty-year-old plastic dome is a short peace. If the unit is recent and the flashing is the only failure, reflashing can be enough. Ask the roofer to price both.
Can I caulk the outside and finish?
Surface caulk at the visible frame is a temporary plug. It rarely reaches the opening that is actually letting water under the shingles, and it has to be removed for a real flashing job.
Why does it only leak in wind?
Wind pushes rain uphill under a head flashing that gravity alone would drain. That pattern points to flashing geometry, not a hole in the middle of the pane.
Take Care Nest publishes general information for homeowners. It is not an inspection, a bid, or a substitute for a licensed contractor. Where the structure may be unsafe, get a qualified professional on site before anyone walks the roof.