The temple complex contains distinct shrines for Shiva, Vishnu, Brahma, and Parvati. A strict local tradition mandates that devotees must first visit the Kalbhairav (fierce form of Shiva) and Jogeshwari temple before entering the main Harihareshwar shrine, and then visit Kalbhairav again before leaving. The architecture is a mix of laterite stone and traditional coastal woodwork.

Harihareshwar was the Kuladaivat (family deity) of the Peshwas. After Peshwa Bajirao I successfully burned down the naval fleet of the Siddis of Janjira in 1723, he heavily patronized the temple, rebuilding its main stone structures and adding the intricate wooden sabha mandap as a gesture of gratitude.