Need photos from outside.

Did the chimney leak before the re-roof?

Picture attached, I do not think it leaked before the re-roof, it leaked during the rain.

Sorry for your issues, how frustrating. Sad reality is that most chimneys are a leak waiting to happen, reason #2 why I recommend people don't include them in their builds or rip them out during reroofing. Reason #1 is that they are terrible for energy efficiency and indoor air quality. Even considering you just reroofed I suggest you decommission your antiquated, inefficient fireplace and remove the chimney above the roof. Many problems solved.

Your best bet for tracking down the leak is to hire a third party who specializes in this sort of sleuthing. It will be hard for us to do from pictures alone. Harrison McCampbell is a forensic architect who writes excellent articles on these subjects like best practices of brick veneer.

I'm guessing the brown flashing is saw cut into the masonry. It's the most common way with current construction practices but is prone to leaking. It could also be your chimney cap. A mason friend of mine is doing these continuous chimney caps, which are an improvement but don't address the chimney to roof flashing.

I don't think it's fair that roofers (or homeowners) end up liable for builders/masons shoddy, cheap work. In cheap builders defense, most homeowners don't seem interested in the cost of true craftsmanship in our current construction market.

Tough to say without a close up but that doesn't look like it was cut into the masonry and trim coil seldom works well in that application. Looks more like gobs of caulk at the joint but again without a close up almost immpossible to be sure. BUT if it didn't leak before the new roof, common sense would lead you to the answer.....................

How old is the house? Are the chimney flues lined? I would suspect the chimney above the roof especially the top if its parged.

house is 27-year old, I think flues lined. leaks during the rain only.

Get someone to inspect the liners.

Is there a proper cricket on the uphill side of the chimney?

The most important thing I've learned about roofs is you can't see anything important from the ground.

It has to be improper flashing done by the roofer.

went up to the roof for the first time, When the roofer just came for caulking the flashing.There is a gap on the chimney on the first picture. bricks are still wet in some areas on the second picture. The chimney guy didn't tell me there were cracks and applied the waterproofing regardless two weeks ago. So the leaking should be coming from those gaps/cracks, right? as some of the cracks are still showing wet from yesterday's rain. other areas w/o cracks are dry.

The joints were originally tooled with a "weather" joint meaning there is a recess at the top of the joint but none at the bottom. That creates a strong shadow line. But the joint mortar has deteriorated and been patched poorly. It wouldn't be too difficult to rake the mortar back and strike the new mortar with dowel to create a more durable concave joint.

@RES, thanks for the advise. is there any temperature restriction for this job? I do not trust the chimney guy any more, they did not identify the cracks and just ripped me off with $900 for waterproofing and crown coat.

She said a chimney guy put a waterproofing coating on the top f the chimney and a roofer came to seal the flashing and check the roofing.

Hold on, I just realized the above comment is an ad for a roofing company.

We can see that there is a cricket--that's good. And counterflashing on the chimney. Question is, are you sure that step flashing was installed? Shingle tabs often cover the step flashing on the roof and the counterflashing would hide it on the chimney. You need to make sure that step flashing was installed.

I would caulk the cracks. Lexel (available at Lowe's) can be applied to wet material and extreme temperature (down to 0 degrees)...so good choice for this time of year. I'm not super confident that the cracks are the source of the leaks...probably too cold to break out the garden hose & test?)...but it makes sense to eliminate them as a possibility.

(I would take a good look at the apex of the chimney flashing on the cricket. Looks like it is gapping?)

ETA: is there kick-out flashing at the top of the chimney counterflashing?

For this use Sashco warns that Lexel may have a hard time maintaining adhesion because as the sun comes out and heats up the moisture in the masonry, it will try to escape and may stress the Lexel to the point of failure.

For non-structural repair of mortar Sashco recommends Mor-Flexx. Don't apply to wet mortar or below 40 degrees.

To eliminate the cracks in the brickwork and the flue liner as the cause it would be easier to temporarily cover the chimney.

RES--Makes sense. Glad to know about Mor-Flexx because I'm sure that I've have future uses for it.

Following

1. check if roofer is/was licensed (contractor's license, not business license).

2. get another roofer to inspect & recommend actions

3. Why is roof jack, rubber boot & PVC pipe not painted? PVC is specifically required to be painted in this exposure. To me, this is an indicator of other things.

Those brick cracks are typical. My guess is the roofer added counter flashing is the issue.

Is the leak on the "uphill" side of the chimney? Then its likely the cricket.

Suspect the cricket.

There you go!

@Jeff, after looking at the correct counter flashing instruction in below, I think it was done incorrectly by the roofer. The roofer might put the shingles under the step flashing instead of above, because when I looked up from the attic, I saw shingles (circled area in the picture) which does not make sense if it was above the step flashing, or there was no step flashing installed at all. I saw shingles directly touching the chimney in the attic roof.

Apparently the new shingles 2 years ago were installed over the old shingles otherwise you would not be able to see shingles tight the chimney from above and below.

Roofer had all 70+ 'A' review on angieslist, licensed as Home Improvement Contractor and with 15 years experience, recommended by co-worker. He looked professional from the paper, now how do I get another professional and how to tell which one is the real 'professional' when I interview them? Totally frustrated. I know I can not rely on angieslist or homeadvisor review 100%, but that was the only way to filter for a homeowner w/o much roofing knowledge.

I'll go back to what I said earlier as well about the roof not leaking before he worked on it and now it is leaking. Also, that counterflashing does not look correct to me, and would make me question what else he did or did not do.

The root cause of water intrusion problems can be difficult to diagnose.

Masonry chimneys require periodic maintenance. While the problems you've observed correlate with the installation of the replacement roof, correlation is not causation. There are cracks and degradation of the masonry as others have noted.

I recommend trying to determine whether the problem is with the shingled roof, the chimney or the interface of the chimney and roof. You can do this by having one person in the attic as an observer and one on the roof with a garden hose and using your cell phones to communicate with each other. Start by wetting down the area of the roof between the peak and chimney without directly wetting the chimney and see if the leak appears. If not, then wet the chimney just over the flashing material and check. If not, work your way up the chimney saturating the brick, but trying not to spray water into the joints. Finally check the mortar crown on top of the chimney to see if it's the culprit. As always when working at heights, use appropriate fall protection or enlist the help of a neighbor or relative you're not fond of to work on the roof.

One you've diagnosed the problem, you can then focus on the best way to address it.