- Agsubay River, a stream in Province of Capiz, Western Visayas
- Aguisan River, a stream
- Aquirre Bank, a bank in Province of Sulu, Autonomous Region in Muslim Mindanao
- Bagacay Bay, a bay in Province of Iloilo, Western Visayas
- Bagacay Creek, a stream in Province of Masbate, Bicol
- Bagacay River, a stream in Province of Surigao del Norte, Caraga
- Bagaguining River, a stream in Province of Masbate, Bicol
- Barotac Bay, a bay in Province of Iloilo, Western Visayas
- Bongao Channel, a marine channel in Province of Tawi-Tawi, Autonomous Region in Muslim Mindanao
- Bongo Shoal, a shoal in Province of Maguindanao, Autonomous Region in Muslim Mindanao
- Bongogon River, a stream in Province of Negros Occidental, Western Visayas
- Bongquirogon River, a stream in Province of Leyte, Eastern Visayas
- Buluangan River, a stream in Province of Negros Occidental, Western Visayas
- Cabug Creek, a stream in Province of Negros Occidental, Western Visayas
- Calog Creek, a stream in Province of Negros Occidental, Western Visayas
- Cantilan River, a stream in Province of Surigao del Sur, Caraga
- Cantilan Shoals, a shoal in Province of Surigao del Sur, Caraga
- Cantomao River, a stream in Southern Leyte, Eastern Visayas
- Creek Tanawan, a stream in Province of Negros Occidental, Western Visayas
- Da-og River, a stream in Province of Negros Oriental, Central Visayas
- Dagoyo Creek, a stream in Province of Negros Oriental, Central Visayas
- Eyamjo River, a stream in Province of Surigao del Sur, Caraga
- Falls Creek, an intermittent stream in Province of Negros Occidental, Western Visayas
- Faoil River, an intermittent stream in Province of Guimaras, Western Visayas
- Favorite Bank, a bank in Province of Sulu, Autonomous Region in Muslim Mindanao
- Glan Peidu Creek, a stream in Province of South Cotabato, Soccsksargen
- Guilis Creek, a stream in Province of Negros Occidental, Western Visayas
- Ilacaon Channel, a marine channel
- Kamawi Shallows, a shoal in Province of Sulu, Autonomous Region in Muslim Mindanao
- Kapon Bay, a bay in Province of Tawi-Tawi, Autonomous Region in Muslim Mindanao
- Klinan River, an intermittent stream in Province of South Cotabato, Soccsksargen
- Kling River, a stream in Province of Sarangani, Soccsksargen
- Kraan River, a stream in Province of Sultan Kudarat, Soccsksargen
- Kuayan River, a stream in Province of Zamboanga del Sur, Zamboanga Peninsula
- Lake Suba, a lake in Province of Sulu, Autonomous Region in Muslim Mindanao
- Lipundan Bay, a bay in Province of Samar, Eastern Visayas
- Lipusan Bay, a bay in Eastern Samar, Eastern Visayas
- Liradao River, a stream in Province of Davao del Sur, Davao
- Liscum Bank, a bank in Province of Zamboanga del Sur, Zamboanga Peninsula
- Lisub Cove, a cove in Province of Surigao del Norte, Caraga
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- Litalit Bay, a bay in Province of Surigao del Norte, Caraga
- Litap River, a stream in Province of Sultan Kudarat, Soccsksargen
- Litoban River, a stream in Province of Zamboanga del Norte, Zamboanga Peninsula
- Little Caliban River, a stream in Province of Negros Occidental, Western Visayas
- Little Layauan Bay, a bay in Province of Surigao del Norte, Caraga
- Mainit River, a stream in Province of Davao del Sur, Davao
- Maitom River, a stream in Province of Leyte, Eastern Visayas
- Makar Cove, a cove
- Makar River, a stream in Province of South Cotabato, Soccsksargen
- Margus Pequeno River, a stream in Province of South Cotabato, Soccsksargen
- Maribojoc Bay, a bay in Province of Bohol, Central Visayas
- Maridagao River, a stream
- Marihatag River, a stream in Province of Surigao del Sur, Caraga
- Marisibong River, a stream
- Nalus River, a stream in Province of Sarangani, Soccsksargen
- Nama River, a stream in Province of Sarangani, Soccsksargen
- Namanyan River, a stream in Province of Negros Occidental, Western Visayas
- Pamay Bay, a bay in Province of Surigao del Norte, Caraga
- Pambu Khan River, a stream in Northern Samar, Eastern Visayas
- Pambuhan Harbor, a harbor in Eastern Samar, Eastern Visayas
- Pambuhan River, a stream in Eastern Samar, Eastern Visayas
- Pamonawan River, a stream in Province of Leyte, Eastern Visayas
- Pasaland Creek, a stream in Province of Negros Occidental, Western Visayas
- Pisalat Creek, a stream in Province of Maguindanao, Autonomous Region in Muslim Mindanao
- Piso River, a stream in Province of Davao Oriental, Davao
- Port Aguirre, an anchorage in Province of Samar, Eastern Visayas
- Port Bongao, an anchorage in Province of Tawi-Tawi, Autonomous Region in Muslim Mindanao
- Salesep River, a stream in Province of Masbate, Bicol
- Salog Bay, a bay in Province of Iloilo, Western Visayas
- Salong, a stream in Province of Negros Occidental, Western Visayas
- Sohutan Bay, a bay in Province of Surigao del Norte, Caraga
- Sohutan Inlet, an inlet in Province of Surigao del Norte, Caraga
- Sowali River, a stream in Province of Negros Occidental, Western Visayas
- Tanaldan River, a stream in Province of Zamboanga del Sur, Zamboanga Peninsula
- Tanao River, a stream
- Tausan Mariki Channel, a marine channel in Province of Tawi-Tawi, Autonomous Region in Muslim Mindanao
- Teomabal Lake, a lake in Province of Sulu, Autonomous Region in Muslim Mindanao
- Tuguis Creek, an intermittent stream in Province of Negros Occidental, Western Visayas
- Tuyom River, a stream in Province of Negros Occidental, Western Visayas
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