The Agusan Marsh is the 1009th RAMSAR site, a wildlife sanctuary which serves as wintering ground for migratory and wetland birds from Asian and Western countries, and is considered one of the most ecologically significant wetland ecosystems in the Philippines. This study assessed species diversity and distribution of birds in four habitat types of the Agusan Marsh. Sago, Terminalia, Mixed Swamp and Peat Swamp forests in the Marsh were surveyed from August 2005 to January 2006 using a combination of mist netting (3,337 net days) and transect walk methods. One hundred twenty-six species of birds were identified consisting of 26 migrants, 69 non-endemics, and 31 endemics (23.81% endemism) of which seven species are categorized as threatened. The Mixed Swamp Forest had the highest species richness (S=92) while the Peat Swamp Forest had the highest number of migratory birds (S=26). Highest endemicity was recorded in the Terminalia Forest (20.63%) while the Sago Forest had the least number of bird species. Migratory birds were recorded at the start of sampling in August, their numbers considerably increasing thereafter and reaching a peak in November. In contrast, the number of endemic species declined in the same month. Previously recorded only in Luzon, the migratory Siberian Rubythroat (Luscinea calliope) was also found in Agusan Marsh, indicating that this bird may be found in other places in the Philippines. Forty-six species of birds, which include six migratory species, were reported to be of socioeconomic importance. Changes in structural and floristic composition brought about by forest degradation, such as conversion of forest into agriculture, logging and hunting, were seen as threats to the birds in Agusan Marsh. Results indicate that the Marsh supports a considerable number of endemic, threatened, and migratory bird species. Conservation of the different Marsh habitats is necessary for the protection of the broadest avifaunal diversity.

The Butuan coastal plain is a fan-delta formed by deposition of Agusan River sediments in the past 7,400 radiocarbon years (ky). Traces of paleochannels that scar the coastal plain, seen in satellite images, indicate past river positions. Immediately prior to the present, Masao River was the active distributary as suggested by its well-defined and still continuous paleochannel. Numerous sudden shifts of river position have likely originated in the San Vicente area, the apex region of the fan-delta. These shifts could have been self driven or induced by floods or tectonics. Sediment input from rivers along the eastern flank of the Butuan coastal plain forced a number of downstream shifts. The function of the Agusan Marsh in buffering flashy river discharges in the Butuan coastal plain is threatened by present-day elevated sediment loads of rivers upstream.

An important region of biodiversity in the country is the Agusan Marsh, located in northeastern Mindanao, southern Philippines. The Marsh aquatic fauna are not well studied and majority of available information is dispersed and sporadic. This study presents an updated systematic list comprising aquatic faunal species collected from seven Marsh localities during a 2006 survey. Of a total of 64 species of aquatic fauna distributed in 45 genera and 37 families, about 59.3% are fishes, 17.2% crustaceans, 14.1% molluscs, and 9.4% reptiles. Most of the aquatic fauna are native and migratory. Flowing rivers, lakes and creeks are the primary habitats of these organisms; majority of them thrive in lakes and upper streams. Fish species reported in earlier literature are also included. The Indigenous Knowledge System (IKS) was applied to integrate species known to the native Manobo, but not found in earlier studies nor the present survey. Fishery-related problems include the decline in fishery stocks, displacement of native species, and destruction of habitats. These problems are attributed to illegal fishing (e.g., electrofishing, use of chemicals and ichthyotoxic plants), overfishing, introduced or exotic or invasive alien species, pollution (e.g., heavy metal contamination), habitat degradation (e.g., conversion of marshland to agriculture), and human disturbance. The deliberate or accidental introductions of exotic species such as carps and the janitor fish now pose serious threats to species diversity. Conservation measures and strict enforcement of wildlife and environmental laws are needed to save the biodiversity of Agusan Marsh for future generations.

The Agusan Marsh is an extensive floodplain in the middle of the Agusan River Basin in eastern Mindanao where rivers, creeks and tributaries mainly in the provinces of Agusan del Norte, Agusan del Sur and Compostela Valley converge and drain northward to the Agusan River and into Butuan Bay. The main habitats of the Marsh are the freshwater swamp forest (with Terminalia, peat swamp and sago palm forest subtypes), secondary scrub, herbaceous swamp, open water (oxbow/floodplain lakes, pools), and flowing water (rivers, streams). Peat forests have been confirmed in Bunawan and Caimpugan. Over 200 bird species have been known to spend at least part of the year in the Marsh, making it an important site for migratory birds from northern Asia and Siberia. As one of the Philippines' ecologically significant wetlands, the Marsh has been declared a protected site under NIP AS (1994), Presidential Proclamation 913 (1996), and RAMSAR (1999). The Agusan Marsh Wildlife Sanctuary covers -111,540 ha in 8 municipalities of Agusan del Sur. Recently the Agusan Marsh was placed high on the list of Philippine nominations to the World Heritage Natural Sites. Despite all these, very few scientific studies have been conducted on the Marsh but this has not stopped drainage and development for agriculture, construction of dams and reservoirs for irrigation, deliberate or accidental introductions of exotic species, e.g., tilapia, carps, janitor fish, and golden apple snail, and logging in the watershed areas. The latter have been legitimized by Integrated Forest Management Agreements despite the presence of primary forests. The latest proposed intervention is the Agusan River Basin Development Project. There is need for scientific research to provide baseline information on hydrology, sediment dynamics and ecology as prerequisite to any interventions and developments in the Agusan Marsh.