Approximately 2 million years ago, the area of preset-day Butuan City was entirely covered by sea. The Agusan River that flowed from the Diwata mountain range empted directly to Butuan Bay and had carried with the sand, silt and clay. These formed a delta which expanded and transform in the area from a marine environment to a coastal plain. Swamps, marshes, streams and estuary were formed.
The growth of the delta divide the direction of the flow of Agusan River and created a new river in the western part of Butuan City. This is the Masao River that serves as the direct source of freshwater for the estuary.
During the 9th and 10th century A.D. the estuary became an ideal and important sanctuary for seafarers. Settlements existed along the estuary shorelines. However this estuary slowly changed into a swampy and marshy environment. Sand, silt and clay blanked the estuary with the floodwaters of the Masao River.
Time and floods created a widespread blanket of sand, silt and clay forming a wide coastal plain in the entire Butuan City area. The present flood behavior of Agusan and Masao Rivers indicate that they still reach the height sufficient enough to flood Butuan City.
