Inspect the chimney thoroughly to find places where water may be entering. Look for cracks in the chimney cap, in the mortar between bricks, missing mortar or bricks, loose flashing around the base of the chimney and damaged shingles in the area of the chimney. Look down the flue with a flashlight to check the condition of the chimney liner.
Pry off the flashing, if you determine it is the problem, with a flat head screwdriver. The top edge of chimney flashing is set into the mortar between bricks so be careful not to damage any bricks when doing this.
Apply roofing tar to the joint between the bricks where the chimney flashing was then reinsert the chimney flashing into the joint.
Apply roofing tar to the joint between the flashing and the chimney bricks all the way around the chimney.
Replace the shingles in the vicinity of the chimney if they are deteriorating or showing signs of water damage.