The most effective flashing is made up of two elements, the flashing and the counter- flashing. The base flashing is an L shaped piece of metal extending up the chimney side and under the roofing shingles. The counter flashing, which overlaps the base flashing, is imbedded and sealed in the chimney's masonry joints. This two element flashing allows both the roof and the chimney to expand or contract at their own rates without breaking the waterproof seal in either area. Most masonry materials are porous and will absorb large amounts of water.
Common brick is like a sponge, absorbing water and wicking moisture to the chimney interior.
Defective mortar joints or the use of improper mortar or brick can greatly increase the tendency to absorb and convey water to the interior of the masonry chimney structure. Several products have been developed specifically for use as waterproofing agents on masonry chimneys. These formulas are vapor permeable which means that they allow the chimney to breathe out, but not in. Thus water that has penetrated the chimney, or moisture that has originated from inside, is allowed to escape, while the waterproofing agent prevents water from entering from the outside. Paint, or any non vapor permeable water sealer, should never be used as a waterproofing agent because it will trap moisture inside the chimney, accelerating deterioration.