Paoha Island is located in the central part of Mono Lake, slightly closer to the western shore. It is a roughly oval-shaped landmass 2 miles (3.2 km) north-south and 1.5 miles (2.4 km) east-west. It is separated from Negit Island, to the north-northwest, by a narrow channel. During low water levels, Negit Island and eventually Paoha Island become connected to the mainland in one giant peninsula.

The island is more mountainous near the east side, with the highest volcanic domes rising more or less than 200 feet (61 m) above the lake surface. The highest cone, which contains the heart-shaped crater lake, is located at the far northeastern end of the island. Several small islets are located off the island's west and south shores.