Chimney and skylight leaks: causes, fixes and costs

Published September 24, 2026 · Updated October 13, 2026

Why chimneys leak

Step and counter flashing

GAF, the shingle maker, describes the system: L-shaped step flashing woven in with each course of shingles up the sides of the chimney, and counter flashing set into the brick above it to cover the top edge. Flashing "can deteriorate over time and become damaged or loose, which can lead to leaks." On older Royal Oak homes it's common to find the counter flashing replaced by a bead of tar or caulk, which cracks after a few winters.

No cricket behind a wide chimney

Water and snow pile up on the uphill side of a chimney. A cricket (or saddle) is a small peaked roof behind it that splits the water around the sides. GAF's guidance cites the International Residential Code, the model for Michigan's residential code, as calling for a cricket when the chimney is more than 30 inches wide. Many older chimneys were built without one.

The crown, cap and brick

The concrete crown on top of the chimney cracks with freeze-thaw cycles, and a missing cap lets rain straight down the flue. Water that gets into the masonry from above can show up inside as a roof leak even when the flashing is sound. That's a mason's job, not a roofer's, so ask the roofer to say which it is.

Why skylights leak

VELUX, the skylight maker, says installation is today's main cause of skylight leaks: an opening cut to the wrong size, or the wrong flashing for the unit. Hail can damage the glass, and re-roofing around an old skylight can disturb it in its frame.

Old plastic bubble skylights and skylights with sealant-only flashing are the usual culprits on Royal Oak homes. VELUX says many of its skylights last 20 years or more and suggests upgrading after about 30.

Leak or condensation?

In a Michigan winter, warm, moist indoor air meets cold glass, and water can run down the inside of the skylight and drip off the frame. Clues that it's condensation: it happens on cold days rather than during rain, the inside of the glass is fogged, and it stops when the weather warms. Water that appears during rain or snowmelt, or stains spreading on the ceiling around the light well, point to a real leak.

How to narrow down the source

• Note when it drips: during rain, wind-driven rain from one direction, snowmelt, or cold dry days
• Look in the attic with a flashlight for wet wood or stains on the chimney's sides or the skylight's light well
• From the ground, look for tar or caulk where metal flashing should be, a cracked crown, or a missing chimney cap
• Photograph the stain inside and the roof outside, and keep a note of dates

Water travels along rafters before it shows, so the stain isn't always below the leak. The roof leak repair page explains what to do right now.

The right fix

For a chimney, a lasting repair usually means new step flashing worked in with the shingles and new counter flashing ground into the mortar joints, not another layer of sealant. A wide chimney with no cricket may need one built. If the crown or brick is the problem, a mason repairs it.

For a skylight, it's new flashing, a new unit, or both. VELUX's advice is to plan on replacing skylights when you replace the roof, so the flashing and the roof go on together and the warranties line up. GAF likewise says to replace the flashing at the same time as the roof.

What chimney flashing and skylight repairs cost

Published chimney and skylight repair prices

Prices as published, checked October 12, 2026 (C & G's on September 27, 2026). C & G describes its figures as typical for common repairs in Royal Oak. HomeAdvisor's are national, updated June 2026. Rebuilding flashing around a large brick chimney, building a cricket or replacing rotten decking costs more.

The roof repair cost guide lists other common repairs and what pushes the price up.

Questions about chimney and skylight leaks