- Agtulasi Creek, a stream in Province of Iloilo, Western Visayas
- Aguada Bay, a bay in Province of Tawi-Tawi, Autonomous Region in Muslim Mindanao
- Aguada Channel, a marine channel in Province of Tawi-Tawi, Autonomous Region in Muslim Mindanao
- Anilao River, a stream in Province of Iloilo, Western Visayas
- Bacuag River, a stream in Province of Surigao del Norte, Caraga
- Baculin Bay, a bay in Province of Davao Oriental, Davao
- Bacun River, a stream
- Bacung River, a stream in Province of Tawi-Tawi, Autonomous Region in Muslim Mindanao
- Bacutcut Bank, a bank in Province of Tawi-Tawi, Autonomous Region in Muslim Mindanao
- Baleno River, a stream in Province of Masbate, Bicol
- Baliton River, a stream in Province of South Cotabato, Soccsksargen
- Bantayan Bay, a bay in Northern Samar, Eastern Visayas
- Bantayan River, a stream in Northern Samar, Eastern Visayas
- Bayang River, a stream in Province of Bohol, Central Visayas
- Bito River, a stream in Province of Leyte, Eastern Visayas
- Bituca River, an intermittent stream in Province of Cebu, Central Visayas
- Butara Creek, a stream in Province of Maguindanao, Autonomous Region in Muslim Mindanao
- Butbut River, a stream in Province of Samar, Eastern Visayas
- Buteren Creek, a stream in Province of Maguindanao, Autonomous Region in Muslim Mindanao
- Butilan Marsh, a marsh in Province of Maguindanao, Autonomous Region in Muslim Mindanao
- Cagbatang River, a stream in Province of Masbate, Bicol
- Cagbatuan River, a stream in Province of Leyte, Eastern Visayas
- Cagbo Creek, a stream in Province of Masbate, Bicol
- Camaroboan River, a stream in Province of Samar, Eastern Visayas
- Cambacamba Channel, a marine channel in Province of Tawi-Tawi, Autonomous Region in Muslim Mindanao
- Chambers Knoll, a shoal in Province of Tawi-Tawi, Autonomous Region in Muslim Mindanao
- Dalican Creek, a stream in Province of Maguindanao, Autonomous Region in Muslim Mindanao
- Dianay Creek, a stream in Province of Negros Occidental, Western Visayas
- Ebpanan Marsh, a marsh in Province of Maguindanao, Autonomous Region in Muslim Mindanao
- Hubason River, a stream in Province of Surigao del Sur, Caraga
- Hubo River, a stream in Province of Surigao del Sur, Caraga
- Hulip River, a stream in Province of Davao del Norte, Davao
- Jambayan River, a stream in Province of Samar, Eastern Visayas
- James Patch, a shoal in Province of Tawi-Tawi, Autonomous Region in Muslim Mindanao
- Janabatas Channel, a marine channel in Province of Leyte, Eastern Visayas
- Jangan River, a stream in Province of Masbate, Bicol
- Jubasan River, a stream in Northern Samar, Eastern Visayas
- Katadungan River, a stream in Province of Maguindanao, Autonomous Region in Muslim Mindanao
- Katapo River, a stream in Northern Samar, Eastern Visayas
- Lajong River, a stream in Province of Masbate, Bicol
- Liang River, a stream in Southern Leyte, Eastern Visayas
- Lianga Bay, a bay in Province of Surigao del Sur, Caraga
- Lianga River, a stream in Province of Surigao del Sur, Caraga
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- Libae Creek, a stream in Province of Surigao del Sur, Caraga
- Look Tua Cove, a cove in Province of Tawi-Tawi, Autonomous Region in Muslim Mindanao
- Loom River, a stream in Eastern Samar, Eastern Visayas
- Loonan Bay, a bay in Province of Surigao del Norte, Caraga
- Luguimi River, a stream in Province of Zamboanga del Sur, Zamboanga Peninsula
- Malagos River, a stream in Province of Davao del Sur, Davao
- Malogo River, a stream in Province of Negros Occidental, Western Visayas
- Manapla River, an intermittent stream in Province of Negros Occidental, Western Visayas
- Manara Diotay River, a stream in Province of Negros Occidental, Western Visayas
- Manara River, a stream in Province of Negros Occidental, Western Visayas
- Marimojon Creek, a section of stream in Province of Iloilo, Western Visayas
- Marintoc River, a stream in Province of Masbate, Bicol
- Nahalugan River, a stream in Northern Samar, Eastern Visayas
- Nahaon River, a stream in Southern Leyte, Eastern Visayas
- Nahulid River, a stream in Southern Leyte, Eastern Visayas
- Naiba Creek, a stream in Province of Iloilo, Western Visayas
- Nusa Tacbu Channel, a marine channel in Province of Tawi-Tawi, Autonomous Region in Muslim Mindanao
- Oak River, an intermittent stream in Province of Masbate, Bicol
- Palapag Channel, a marine channel in Northern Samar, Eastern Visayas
- Palapag River, a stream in Northern Samar, Eastern Visayas
- Pigut Passage, a marine channel in Province of Surigao del Norte, Caraga
- Port Palapag, an anchorage in Northern Samar, Eastern Visayas
- Progreso Creek, a stream in Province of Masbate, Bicol
- Rio Grande, a distributary
- Sapalan Creek, a stream in Province of Maguindanao, Autonomous Region in Muslim Mindanao
- Senonoc River, a stream in Province of Surigao del Norte, Caraga
- Serantes Shoal, a shoal in Province of Sulu, Autonomous Region in Muslim Mindanao
- Serenaya River, a stream in Province of North Cotabato, Soccsksargen
- Serruco River, a stream in Province of Iloilo, Western Visayas
- Sondara River, a stream in Province of Samar, Eastern Visayas
- Tacu Shoal, a shoal in Province of Masbate, Bicol
- Taft River, a stream in Eastern Samar, Eastern Visayas
- Tag-abaca River, a stream in Province of Leyte, Eastern Visayas
- Tagabaka Cove, a cove in Province of Surigao del Norte, Caraga
- Tambulig River, a stream in Province of Zamboanga del Sur, Zamboanga Peninsula
- Tambunac River, a stream in Province of Iloilo, Western Visayas
- Tianbuligue River, a stream in Province of Zamboanga del Sur, Zamboanga Peninsula
- Tibo River, a stream in Province of Leyte, Eastern Visayas
- Tibungoy Creek, a stream in Province of Davao del Sur, Davao
- Ticao Bay, a bay in Province of Masbate, Bicol
- Tubay Creek, a stream in Province of Sarangani, Soccsksargen
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