Deep dive · Updated October 17, 2026

Skylights and flashing: the most common roof leak points

Ask roofers where leaks start and most will say flashing. Skylights, chimneys, valleys and walls are where roofs are most often interrupted, and where water finds its way in.

What flashing does

Flashing is thin metal (or sometimes membrane) that directs water away from joints. Common types include:

• Step flashing: L-shaped pieces woven with shingles along walls and chimneys
• Counter-flashing: covers step flashing, set into masonry or siding
• Valley flashing: lines the valley where two slopes meet
• Drip edge: at eaves and rakes
• Pipe boots: around plumbing vents

Why flashing fails

• Age and corrosion, faster near the coast in Sausalito, Tiburon and Belvedere
• Sealant used in place of proper flashing, which degrades in sun
• Reroofs that reused old flashing
• Movement between chimney and roof
• Cracked rubber vent boots

Skylights

Skylight leaks come from flashing, from failed seals, or from condensation:

• Flashing leak: appears during rain, often on one side
• Seal failure: fogging between panes, or drips from the frame
• Condensation: forms on cold mornings and drips evenly from the glass. It's common with older single-pane or plastic dome units in Marin's damp months.

See roof leak vs. condensation.

Chimneys

Older brick chimneys in San Anselmo, Ross, Mill Valley and San Rafael often have aging flashing, cracked crowns or deteriorating mortar. A chimney leak can come from the flashing or from the masonry itself.

Proper repair

• Replace damaged flashing rather than piling on sealant
• Integrate new flashing with the roofing and underlayment
• For skylights, consider whether replacing an aging unit (with a manufacturer flashing kit) makes more sense than repairing it
• For low-slope roofs, flashing at walls and curbs should follow the membrane manufacturer's details

When reroofing

Ask whether all flashing will be replaced, how skylights and chimneys will be handled, and whether new vent boots are included.

Skylight types and their typical problems

• Plastic domes (common on older mid-century homes): can craze, crack and yellow. The curb flashing is often a weak point.
• Older glass units with failed seals: fogging between panes, and sometimes leaks at the frame.
• Modern curb-mounted or deck-mounted units: usually installed with manufacturer flashing kits. Problems typically come from installation errors or debris buildup on the uphill side.
• Tubular skylights: small penetrations, usually reliable if flashed properly.

Repair or replace a skylight?

Replacing an aging skylight is often recommended during a reroof, because the flashing has to be redone anyway and newer units are typically designed to integrate with modern flashing systems. Outside of a reroof, repairing flashing on a sound skylight can make sense. Ask your roofer about both options.

Chimney flashing in detail

A properly flashed brick chimney usually has:

• Step flashing along the sides, woven with shingles
• Counter-flashing set into mortar joints, covering the step flashing
• A cricket (saddle) on the uphill side of wider chimneys to divert water and debris
• A sound crown on top, to keep water out of the masonry

Missing crickets, cracked crowns and counter-flashing simply caulked to the brick face are common findings in older Marin homes.

Wall transitions on additions

Many Marin homes have additions where a roof meets a two-story wall. These need step flashing behind the siding plus "kick-out" flashing at the bottom edge to direct water into the gutter instead of behind the siding. A missing kick-out is a common cause of rot and leaks at the corner where the roof meets the wall.

Valleys

Valleys carry a lot of water and collect debris. Open metal valleys and "closed-cut" shingle valleys are both common. Either way, keep them clear, especially under trees.

Why sealant isn't a fix

Roofing sealant, often called caulk or roof cement, has its place, but it breaks down in sun and with movement. Leaks "fixed" with sealant often return within a season or two. Lasting repairs replace or properly install the flashing itself.

Skylight condensation fixes

If your skylight drips from condensation rather than a leak:

• Improve ventilation in the room, especially bathrooms
• Use a dehumidifier in damp seasons
• Consider replacing old single-pane or dome units with insulated glass

Before you hire

Ask to see photos of the flashing problem, ask whether flashing will be replaced or sealed, and check the license on the CSLB site.

A quick seasonal check

Each fall, look at skylights and chimneys from the ground with binoculars. Check for debris piled on the uphill side, rust streaks, missing or lifted counter-flashing, and cracked domes. Indoors, look for stains on skylight wells and around the chimney breast. Catching a flashing problem in October is far cheaper than chasing a leak in January.

Also check the skylight's interior well for peeling paint or soft drywall after storms. That's often the first sign of a slow flashing leak that never reaches the floor.

Related reading

• Leak detection
• The complete roof guide
• Roof leak repair

Frequently asked questions

This guide is general information, not legal, insurance or medical advice. Sources are linked in the text. Marin Roof Repair is a referral service and doesn't perform the work.