Skylight Leaks: Repair or Replace?

Most leaking skylights do not need to be replaced. They need new flashing. Eight times out of ten, water is getting in around the unit, not through it. A flashing repair runs $300 to $800. A full replacement runs $1,500 to $3,500. Knowing which one you actually need saves real money.

Here is how to tell the difference, when each fix is right, and what Bay Area homeowners should expect to pay either way.

Step One: Confirm It Is a Leak

Skylights produce condensation, especially in winter. People often mistake condensation for a leak and pay for repairs they did not need. Two quick checks tell you which one you have.

Timing. Condensation appears on cold mornings and disappears as the day warms up. A leak shows up during rain or right after, and the water keeps coming as long as it is wet outside.

Location. Condensation forms on the inside of the glass and runs down the frame. A leak typically shows on the ceiling, drywall, or trim around the skylight. Stains, bubbling paint, or a soft spot in the drywall confirm a leak.

Fog belt homes in Pacifica, Daly City, and parts of San Francisco get heavy condensation through winter. Adding bath fans, fixing attic ventilation, and improving the seal around the skylight curb usually fixes condensation issues without touching the unit itself.

Where Skylight Leaks Actually Come From

There are four spots where water gets in. Knowing which one is failing tells you whether you need a $400 fix or a $3,000 fix.

1. Flashing (most common)

Flashing is the metal that wraps the skylight curb and ties it into the surrounding roof material. When it fails, water runs under the shingles or tiles and into the attic. This is the leak source 70 to 80 percent of the time.

Signs: stains on the ceiling near the skylight edge, water dripping at the corners of the frame, attic insulation wet around the curb. Flashing repair or replacement is the fix.

2. Glass seal failure

Modern skylights have a sealed double-pane glass unit. When the seal between panes fails, you see fogging between the panes that does not wipe off. This usually does not cause active leaking, but it indicates the unit is past its useful life and a glass leak is coming.

If you see persistent fog inside the glass, plan for skylight replacement within 1 to 2 years.

3. Cracked dome or glass

Plastic dome skylights crack from UV exposure, especially in inland Tri-Valley heat. Livermore, Pleasanton, and Gilroy homeowners with 1980s and 1990s acrylic domes see this often. A visible crack or yellowing dome means the skylight needs replacement. Glass skylights crack from impact (falling tree limbs, hail).

4. Curb rot

The wooden curb that the skylight sits on rots when chronic leaks have gone unaddressed. By the time you see warped trim or soft wood, you are looking at a full skylight replacement plus framing repair. Curb rot is the most expensive scenario, often $3,000 to $6,000 with the carpentry work.

When to Repair

Repair makes sense when these are all true.

• The skylight unit itself is under 15 years old.
• The glass seal is intact (no fogging between panes).
• The leak source is flashing, sealant, or surrounding shingles.
• The curb is sound (no soft or rotted wood).

A typical flashing repair takes a couple of hours and runs $300 to $800. Resealing exposed sealant joints (the cheapest fix) costs $150 to $400 but is more of a stopgap than a long-term solution. Full flashing kit replacement runs $600 to $1,500 and lasts as long as your roof.

When to Replace

Replace the skylight when any of these are true.

• The unit is over 20 years old.
• The glass shows persistent fog or moisture between panes.
• The dome is cracked, yellowed, or distorted.
• The leak has caused interior damage to the curb.
• You want to upgrade to a venting, solar-powered, or impact-rated model.

A direct swap into the existing opening runs $1,500 to $3,500 for a fixed glass skylight. Venting or solar-powered models add $500 to $1,500. Resizing the opening or upgrading to a larger unit pushes the project to $4,000 to $7,000 because of framing and drywall work.

When to Coordinate with a Roof Replacement

If your roof is within 5 years of end of life, replace the skylights at the same time as the roof. This is the cleanest, cheapest path. The flashing gets installed properly with the new roof material. There are no patches in the surrounding area. And you do not pay for skylight labor twice.

For homes already planning a roof replacement, adding skylight replacement adds about $1,000 to $2,000 per unit. That is significantly less than doing it as a separate project. Most newer homes in Sunnyvale, Mountain View, and Cupertino have 1 to 3 skylights, and bundling them with a roof job is a common move.

Older Spanish-style and Mediterranean homes in Los Gatos and Saratoga often have larger custom skylights or sun tunnels that complicate the math. A roof inspection before the roof project flags any skylight work that should be bundled in.

Common Mistakes to Avoid

The skylight leak space has more bad fixes than almost any other roofing problem. Watch for these.

Mistake 1: Caulk-only repairs. A handyman puts a tube of caulk on the visible seam and calls it done. Caulk is not a flashing system. It works for 6 to 18 months and the leak comes back. Real flashing is the only durable fix.

Mistake 2: Replacing the unit before checking the flashing. If the flashing is the actual leak source, replacing the skylight does nothing. The new unit will leak just like the old one. Always identify the leak source first.

Mistake 3: Ignoring fog between panes. Foggy glass means the seal is gone. The unit is on borrowed time. Replace it before water starts coming through the glass and damaging the interior.

Mistake 4: Skipping inspection of the curb. Active leaks rot wood. Replacing the skylight without checking the curb means you are putting a new $2,000 unit on a rotten frame. The leak comes back within a year.

What a Real Diagnosis Looks Like

A proper skylight leak inspection takes 30 to 60 minutes and includes these steps.

From outside: a roofer checks flashing condition, sealant joints, surrounding roofing material, and the dome or glass for cracks. They look for granule loss around the curb (a sign of water flow patterns) and check whether shingles or tiles have been disturbed.

From inside the attic: they trace water staining back to the source, check the curb wood for soft spots, and look for any related decking damage.

From the room below: they identify staining patterns, condensation behavior, and whether the issue gets worse with wind direction or specific weather conditions.

That diagnosis is what tells you whether you are looking at a $400 fix, a $2,500 fix, or a coordinated roof and skylight project. A professional roof inspection is the starting point for any skylight problem that has been leaking more than once.