During heavy rain, roof leakage can be a common issue for homeowners. Several factors can cause a roof to seep during intense rain, including: If some of the shingles on your roof are broken or missing, rain can get in between them and cause leaks. Flashing is the material used to seal the junctions and margins of your roof. If your flashing is improperly installed or damaged, your roof will leak. If it is inadequately installed or damaged, it can allow precipitation to enter the residence. If