Scappoose Bay is part of the Lower Willamette 4th field Hydrologic Unit Code (HUC). Major sub-basins include Milton Creek, and North and South Scappoose Creeks. Honeyman and McNulty Creeks are smaller sub-basins flowing into the Bay, while Jackson Creek flows through the Scappoose Bay Bottomlands before it drains into the Multnomah Channel. Scappoose Bay flows into the Multnomah Channel just upstream from its confluence with the Columbia River.

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Major Sub-basins of Scappoose Bay

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Scappoose Bay, Sauvie Island, and Multnomah Channel