Approximately two million years ago the area of present day Butuan City was entirely covered by sea. The Agusan River that flowed from the Diwata mountain range emptied directly to Butuan Bay and had carried with it sand, silt and clay. These formed a Delta which expanded and transformed the area from a marine environment to a coastal plain. Swamps, marshes, streams and estuary were formed. The growth of the Delta divided 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 served as the direct source of Freshwater for the estuary.
During the 9th and 10th centuries AD the estuary became an ideal and important sanctuary for seafarers. Settlements existed along the estuary's shorelines. However this estuary slowly changed into a swampy and marshy environment . Sand,silt and clay blanketed the estuary with flood waters of Masao River . Time and floods created a widespread blanket of sand,silt and clay forming a wide coastal plain in the entire Butuan area. The present flood behavior of Agusan and Masao Rivers. indicates that they still reach the height sufficient enough to flood Butuan City.
Butuan City was originally located in Pinamangculan by the banks of the Masao River,about a kilometer from the barrio of Libertad. Finding the place less ideal because of the flood, the people moved to Maug, now the municipality of Magallanes, at the mouth of the Agusan River, they again transferred to Lapaca, now known as Linungsuran in Barrio Banza about five kilometers inland of Agusan River, still troubled by floods, the people once more settled, some eighty years ago, this time permanently, in a higher place called Agao, which is the present site of the City proper.
A description of Butuan is not complete without infusing it with the significance of the Agusan River and its tributaries that provided the valley with rich soil from periodic floods. It's serpentine route through the city and the two Agusan provinces provide the people with easy means of transportation for trade and commerce and encourage settlement along its banks. The Agusan River greatly helped the booming of the Logging Industry which earned Butuan the name "Timber City of the South".
Butuan City sprawls accross the Agusan River nine kilometers from its mouth. Toward this, to the North and seaward, run fertile ricelands. Halfway round the city to the southwest, roll the gently sloping hills over the Mount Mayapay looms. To the east, the majestic Hilong-hilong and Diwata mountain ranges protect the entire valley from fierce Pacific storms.
It is very difficult to pinpoint when the name Butuan first emerged. Certainly the name Agusan came into being upon the creation of the province in 1914 . Before this, the entire area had been known as such as can be born out by old historical records.