Lake Pátzcuaro lies in an endorheic basin, which does not drain to the sea. A watershed area of 929 square kilometres drains into the lake, of which 126.4 are the water body. The Lake Pátzcuaro watershed extends 50 kilometres east-west and 33 kilometres from north to south. Lake Pátzcuaro lies at an elevation of 1,920 metres, and is the center of the basin and is surrounded by volcanic mountains with very steep slopes. It has an average depth of 5 metres and a maximum of 11. Its volume is approximately 580 million cubic metres.
The Lake Pátzcuaro basin is of volcanic origin. At times it has been part of an open and continuous hydrological system formed by Lake Cuitzeo, Pátzcuaro and Lake Zirahuén, which drained into the Lerma River. Today, like lakes Cuitzeo and Zirahuén, it is a closed basin, although ecologists consider it a sub-basin of the Lerma-Chapala basin.