Geologically, a large area was flooded with basalt from volcanic eruptions about four million years ago. Later, vast mudflows–perhaps from early eruptions of Mount Hood–poured down the Sandy River valley and spread out on the plain. More recently in geological time, about 12,000-14,000 years ago, a series of mega-floods of glacial melt water from Montana roared through. Flood water backed up as a vast lake in the lower Columbia River valley, covering it with gravel, sand, silt and clay.

Close to its mouth, the Sandy River split into two channels. In the 1930's, the Oregon Department of Fish diked the main channel, diverting it into the other, believing (in error) that it would help the smelt run. The main channel then filled in with silt. The delta became pastureland, and its wetlands were drained by a series of ditches.