Although you can travel between the major islands (Luzon, visayas, and Mindanao) thru planes, some destinations can only be reached by boat travel. Boats and Ferries also offer a faster alternative to destinations commonly serviced by buses. Small boats and ferries are often called “Bangka” while the bigger boats are called “Bapor” or “Barko” (the term “Barko” usually refers to huge cargo ships). Rafts are referred to as “Balsa” and are mostly used in small rivers and lagoons. It is also worth noting the beautiful “Vinta”, a kind of colorful sailboat found in the Mindanao Region. Though it is not usually used as a form of public transportation, some places in Mindanao offer tourists “Vinta” rides and rentals. Don’t pass up on the opportunity if you ever have the chance.

In Urban manila, small motorized boats and paddle boats called are found along the Pasig River. They usually provide transport for pedestrians to cross the Pasig River, since there are only a few bridges that connect the river banks. There also used to be a small ferry boat traversing through the Pasig river called the "Stracraft" (named as such even before the hugely popular PC game existed) that offers a fast transportation to and from Manila and Laguna, but it went bankrupt. Now, the "Starcraft" project is being resurrected due to the heavy traffic in the roads and the rising cost of fuel and Toll fees. Laguna to Manila by bus often takes 3-4 hours during heavy traffic hours and 1.5 to 2 hours during regular hours. Laguna to Manila by "Starcraft" usually takes only 1 hour any time of the day, or 30 minutes if the trip goes straight from Laguna terminal to Manila terminal non-stop. Manila to Laguna takes a bit Longer, since the trip is upstream. In cities which are prone to floods and have large bodies of water such as Malabon and Navotas, there also are small paddle boats and even rafts to ferry passengers. There is also a place in Navotas often called the "Venice" of Manila since boats are often used to ferry pedestrians in the neighborhood.

Interisland Travel by boats and ferries are easy to find. The three largest liners are Negros Navigation, Sulpicio lines, and WG&A Company (by that order). The central terminal is in the Manila Harbor. WG&A have a fleet of 10 Super Ferry and 2 regular Ferry Boats. They offer travel to and from Manila to other points in the Philippines such as Cebu and Negros Occidental. Super Ferries are preferred by tourist since they are the cleanest and most comfortable and they even provide in-board entertainment. The Super Cat line is a subsidiary of WG&A which has 3 Super Cat ferries which is a type of Catamaran and is extremely fast. Super Cats serves 10 various ports in the Philippines. Negros Navigations is the oldest Boat company in the Philippines, and covers most destinations including trips to Zamboanga, Cebu, and Palawan. They also have the largest boats and the biggest Fleet. Sulpicio Lines also serve routes similar to Negros Navigations but have more ports on various parts of Mindanao. MBRS Lines offer small ferries between Panay and Romblon to Manila. El Greco Jet Ferries have daily trips between Manila and Bataan which offers a faster alternative to a Bus trip since it would only take less than 2 hours rather than 6-8 hours by bus. There are also a fleet of small boats that operate in popular island destinations such as in Puerto Galera, Boracay, and Hundred Islands. In some provinces like in Abra and Negros, there are boats that are used to transport cars between large rivers, since there are no bridges that cross those rivers.