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Why Does Water Enter Around Chimneys and Skylights?

Last updated October 25, 2026

The short answer

Flashing Failures Are the Main Culprit

Flashing is the thin metal or rubber material installed around chimneys and skylights to direct water away. Its job is to bridge the gap between the roof and the vertical structure. If this flashing becomes loose, corroded, or develops small holes, it loses its effectiveness. Water then easily flows underneath it, bypassing your roof's shingles and leading to interior leaks.

The installation quality of flashing is critical. Even new flashing can leak if it is not properly integrated with the roof underlayment and shingles. A common mistake is using the wrong type of flashing for your specific roof material. Overlapping sections incorrectly or using inadequate sealant can create vulnerable points from the very beginning.

How Sealant Breaks Down over Time

Flashing relies on a bead of waterproof sealant, often a caulk or roofing cement, to seal its edges. This material is not permanent. It dries out, becomes brittle, and cracks after years of exposure to sun, rain, and temperature swings. Once the sealant fails, it creates a direct entry point for water to seep behind the flashing.

The process of sealant breakdown accelerates in many climates. Repeated freeze-thaw cycles in winter can widen tiny cracks. Summer heat can soften and degrade some types of sealant. Regular inspection of these sealant beads, especially after extreme weather, can help you spot deterioration before a major leak develops.

Common Issues with Chimney Flashing

Chimney flashing is complex because it must seal a masonry structure that expands and contracts at a different rate than the roof. It typically involves two layers: step flashing along the sides and counter flashing embedded into the chimney mortar. If the mortar joint holding the counter flashing deteriorates, water can run directly down the chimney into your attic or walls.

Another frequent problem is cracked crown or cap on top of the chimney. If this concrete seal is damaged, water enters the chimney chase itself. It can then travel down the interior brickwork and eventually seep out at the flashing level or cause moisture damage inside the fireplace and surrounding walls.

  • Deteriorated mortar joints around counter flashing.
  • Rusted, bent, or missing pieces of step flashing.
  • A cracked or missing chimney crown or cap.
  • Separation where the flashing meets the roof shingles.
  • Improperly sized flashing that does not provide enough coverage.
  • Accumulated debris, like leaves, that traps moisture against the flashing.

Typical Problems with Skylight Installations

Skylights have a built-in curb or frame that must be perfectly flashed. Leaks often occur because the skylight's own flashing kit was not installed according to the manufacturer's instructions. If the unit is not level, water can pool around its base. The constant weight and moisture will eventually compromise the sealant and underlying roof materials.

Condensation is another concern with skylights. The temperature difference between the warm room air and the cold glass can cause moisture to form on the interior. While this is not a roof leak, it can mimic one, leading to water stains on ceilings or walls. Proper ventilation and double-paned glass help reduce this issue.

What to Do When You Discover a Leak

If you see water stains or dripping, contain the interior damage immediately. Place buckets and move furniture. Then, if it is safe, try to trace the water path in your attic to confirm the source is near the chimney or skylight. Avoid going on a wet roof yourself, as it is slippery and you could cause more damage or injure yourself.

Your next step is to contact local water damage pros for water extraction and drying. They have tools to remove water and moisture from walls and ceilings to prevent mold. For the permanent roof repair, you will need a qualified roofer to inspect and repair or replace the failed flashing and sealant. These are two separate trades for two different jobs.

  • Contain interior water with buckets and towels.
  • Safely inspect the attic to help locate the entry point.
  • Contact local water damage pros for drying and moisture control.
  • Hire a qualified roofer for a permanent flashing repair.
  • Document the damage with photos for an insurance claim.
  • Policies vary, and your insurer decides what is covered.

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Frequently asked questions

Can I just caulk the leak myself?

Applying new caulk over old, failed sealant is usually a temporary fix. The underlying problem, like damaged flashing, remains. For a lasting repair, the old sealant must be fully removed and the flashing inspected by a roofer. Improper caulking can even trap water inside, worsening hidden rot.

How can I tell if my flashing is bad?

Visible signs include rust, bent or loose metal, gaps between the flashing and roof, or missing sections. Inside, look for water stains on ceilings or walls near the chimney or skylight. From the ground, you might see lifted shingles or cracked sealant around the base of these structures.

Does homeowners insurance cover this type of leak?

Coverage often depends on the cause. Sudden damage from a storm may be covered, while wear and tear or lack of maintenance typically is not. You must file a claim and an adjuster will assess it. Policies vary, and your insurer decides what is covered. Always check your policy details.

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