[2] In 1990, Filipino shipping conglomerate Magsaysay Lines began operating Metro Ferry as an alternative mode of transport along the Pasig River to alleviate the traffic problem in Manila.

[3] The Metro Ferry operated a route from Guadalupe in then-municipality of Makati down to Escolta Street in Manila, spanning a total length of 15 kilometers (9.3 mi) using river-side sheds as stations and piers constructed by the Philippine Ports Authority.

[citation needed] In 1995, the StarCraft Ferry Corporation submitted proposals to provide passenger services on the river.

A year earlier, however, Uniwide Sales-owned Marilag Transport Systems also submitted a proposal for ferry services not only along the Pasig River but also to and from the province of Cavite and the Baclaran area in Parañaque using foreign-made boats.

[2] In response to concerns about competing ferry operations along the river, President Fidel V. Ramos formed an inter-agency committee composed of national government agencies and local government units to prepare guidelines for ferryboat service on the Pasig River and plan future interconnections with ferry services in Laguna de Bay.

The company operated a 16.2 kilometers (10.1 mi) route spanning the seven stations of Escolta, Lawton, PUP, and Punta in Manila, Hulo in Mandaluyong, Guadalupe in Makati, and Bambang in Pasig.

[citation needed] The current ferry service, the Pasig River Ferry Service, was first inaugurated by President Gloria Macapagal Arroyo on February 14, 2007, that initially covered 15 stations, namely Escolta, Plaza Mexico, Quezon Bridge, PUP, Lambingan, and Santa Ana in Manila, Valenzuela and Guadalupe in Makati, Hulo in Mandaluyong, San Joaquin and Caniogan in Pasig, Riverbanks, Santa Elena, and Marcos Bridge in Marikina, and Napindan in Taguig.

The service was launched with an initial fleet of three catamaran boats operated by private operator SCC Nautical Transport Services Incorporated[5] under a franchise granted by Maritime Industry Authority (MARINA) and an agreement between the Pasig River Rehabilitation Commission (PRRC), Department of Transportation and Communications (DOTC), and Metropolitan Manila Development Authority (MMDA).

In response to the report, the PRRC stated that ferry revenue declined due to a dwindling number of passengers and frequent cancellation of regular trips in order to accommodate river tours.

[6]: 3 In 2018, the Department of Budget and Management (DBM) pitched the Pasig River Ferry Convergence Program, a plan to develop an additional 17 stations in the next four years to serve up to 76,800 passengers daily and to bid out a contract to operate the Pasig River Ferry Service to a private firm.

[11] A 50-seater ferry, M/B Vicente, was also donated to the MMDA by real estate company New San Jose Builders in a turnover ceremony on March 5, 2021.

[citation needed] The Pasig River Ferry Service is open every Monday to Saturday from 6:00 am to 6:00 pm with an average headway of 30 minutes between trips.

[23] The MMDA plans to repair and reopen the Riverbanks station once the Marikina River is confirmed to be navigable for ferry services, and has plans to construct an additional station in the vicinity of the Department of Budget and Management central office and Isla de Convalecencia in San Miguel, Manila, and Intramuros, Manila.

[citation needed] The system formerly used twin-hulled, double-engine catamaran-type ships with a maximum seating capacity of 150 people.

[citation needed] The 2014 iteration of the Pasig River Ferry System operated 14 Manta boats manufactured by the Cebu-based Stordal Marine Corporation.