The commission served for 20 years, from 1999 until its dissolution by President Rodrigo Duterte in November 2019.

The body's powers and functions were transferred to the Manila Bay Task Force and the Department of Environment and Natural Resources.

54 to strengthen the government's program to rehabilitate the river for transportation, recreation and tourism purposes.

54 was signed, an amendment was inserted giving private companies a license to coordinate with the commission concerning the rehabilitation program.

In March 2008, ABS-CBN Foundation Inc. and the Department of Environment and Natural Resources through the Pasig River Rehabilitation Commission signed a memorandum of agreement to co-manage the rehabilitation of the Pasig River and its tributaries.