Skylight Leaks, Stains and Flashing Issues

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Published: March 18, 2014 Last Updated: June 25, 2018

In terms of skylights, flashing is the metal that is installed around the skylight edges to help prevent water from getting in between the skylight and the roof or attic area.

If the skylight is not flashed properly or it is damaged then moisture intrusion may occur. Therefore, maintenance from time to time may be needed. Overall skylights need very little maintenance.

It’s the upside…

It is on the upside of a skylight where many of the problems occur. Snow, leaves and debris tend to gather in and around the skylights’ upside area causing water to back up under the shingles and allowing moisture to intrude. This upside area should be kept clear of debris and maintained well. Usually once a year is sufficient. Doing it in the fall, once the leaves have shed is generally the best time of year to do this.

Rust on the Flashing

When there is rust on the metal flashing it is wise to brush and sand off the loose rust, apply a quality metal rust prohibiting primer, and then repaint with a good topcoat.

Stains below a skylight

One of several reasons for areas near a skylight to be stained is that the flashing needs to be caulked or sealed. This is one of the more common problems that develops with skylights. At times the skylight may be cracked, some of which are hard to see. ( Read more about SKYLIGHT CRACKS )

Occasionally: The condensate gutter (channel) or weep holes are clogged and need cleaning

On the interior of the house, condensate may gather on the bottom side of a skylight; usually when the outside temperature is colder than the interior. In bathrooms when someone takes a long hot shower, in kitchens when boiling water or cooking spaghetti, or when the inside has a high humidity level, is when this often happens. Now, if the skylight has a condensate gutter / channel and it becomes clogged, then staining may occur on the ceiling areas near the skylight. ( Read more on “CONDENSATE GUTTERS AND WEEP HOLES” )


Maintaining skylights is generally easy and inexpensive. Cleaning and checking the skylights on an annual basis helps to prevent leaks and makes the house brighter and more enjoyable. This task would be part of a wise maintenance program for a homeowner.

Skylight specialist and roofers are the two types of contractors who generally do this type of work.

Who to consult? Roofer and skylight installers.

Some repairs and maintenance may be done by home owners and qualified handymen. Roofers and skylight installation companies will also do this work.

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