The present disclosure is directed to a roof mounting system that utilizes a base plate that is affixed to a roof surface by multiple fasteners (e.g., lag bolts, screws etc.) and a cap (e.g., top cap) that attaches to the base plate covering the fasteners affixing the base plate to the roof surface. Once attached, the top cap covers the fasteners preventing water infiltration. To further waterproof the fasteners affixing the base plate to the roof surface, the base plate includes a raised or elevated section on its top surface with a planar flange extending around the elevated section. A portion of the flange may be disposed beneath a single or shingles on a roof surface. The fasteners extend through the elevated section. Accordingly, water drains around the elevated section when the base plate is attached to a roof surface further isolating the fasteners.