What the roofer should have done at the chimney
The Building America Solution Center, a U.S. Department of Energy guide, says that when a home is reroofed, the flashing around every roof penetration, chimneys included, should be inspected and replaced or added as needed. So ask the roofer plainly: was the chimney flashing replaced, reused or just sealed over? Then check the written contract and any job photos for the same answer.
On a shingled roof, chimney flashing is three parts that overlap: base flashing at the bottom, step flashing woven in with each course of shingles along the sides, and counterflashing on top that is set into a mortar joint in the brick. On the uphill side, a cricket (a small peaked diversion, also called a saddle) should send runoff around it. The chimney guide covers each piece. Flat rowhome roofs use different materials, but the question is the same: how was the roof tied into the brick?
Two red flags come from the National Park Service's Preservation Brief 47: step flashing installed as one long piece where several overlapping pieces are needed, and step flashing held on with mastic or sealant. A fresh bead of caulk along the chimney is not a flashing repair. Our guide to why roof leaks start at the flashing explains the other common failure points.
Clues that point away from the roof
The flashing isn't the only suspect. Brief 47 says a chimney's mortar cap should slope to drain water away from the flue, and it warns against thin mortar washes, which tend to crack and let water into the masonry. Water can also get in through cracked or eroded mortar joints above the flashing, where a roofer working at roof level may never look.
Write down where the water shows up: inside the fireplace, on the face of the chimney, or on the ceiling or wall beside it, and whether it follows long or wind-driven rain. Give that to the inspector as a clue, not a diagnosis.
Watch the wording on estimates, too. "Chimney cap" can mean the masonry top (often called the crown) or a metal rain cover over the flue. They are different repairs. If a rain cover is added, Brief 47 says it must still allow adequate venting and exhaust, so that belongs with a chimney professional.
Mortar repairs on older brick chimneys
If the joints are the problem, the fix is repointing: cutting out worn mortar and packing in new. Mortar that's too hard can damage old brick. The Park Service's Preservation Brief 2 says repointing mortar should be softer, or more permeable, than the brick and no harder than the original mortar, so moisture escapes through the joints instead of the brick. It also says old mortar should come out to at least 2 to 2½ times the width of the joint, about ½ to 1 inch for most brick. Ask a mason what mix they plan to use and why it suits your brick, and whether only the failed joints need work.
What to document before anyone comes out
Stay off the roof. From the ground, zoom in with your phone on the chimney and the metal where it meets the roof. Indoors, photograph every stain and note the date, how long it rained and whether the wind was strong. The Solution Center's flashing checklist shows what proper step flashing and crickets look like, so you can compare.
Dry anything that got wet quickly. The EPA says to dry wet materials within 24 to 48 hours if possible, and not to seal or paint over materials that are still wet or show mold. Our wet drywall guide covers when a ceiling can be saved.
Who to call and what to ask
Start with the roofer, with your contract and photos in hand. Ask what they found at each side of the chimney, whether the problem falls within the work they did, and how they'll prove the fix worked, for example with a controlled water test. If they point to the crown, the mortar or the brick, bring in a chimney or masonry contractor, and ask the two to agree on the order of work so the counterflashing gets reset properly after any masonry repair.
If the fix turns into a bigger roof job on a Philadelphia rowhome, check our guide to when a rowhome roof replacement needs a permit before work is redone.