The main terminal of the Philippine National Railways lies within the city . One commuter railway within Metro Manila is in operation . The line runs in a general north @-@ south direction from Tutuban ( Tondo ) toward Laguna . The Port of Manila , located in the vicinity of Manila Bay is the chief seaport of the Philippines . The Pasig River Ferry Service which runs on the Pasig River is another form of transportation . The city is also served by the Ninoy Aquino International Airport and Clark International Airport .