At Riverside in eastern Malheur County it receives the South Fork Malheur River from the south, then turns sharply back northward to Juntura, where it receives the North Fork Malheur River form the north.
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The name first appears in the record in 1826 when Peter Skene Ogden, a fur trapper with the Hudson's Bay Company, referred to it as "River au Malheur (from rivière au Malheur, literally: River of the Misfortune)" and thereafter as "Unfortunate River."
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The streamflow of the Malheur and its tributaries is heavily influenced by a complex system of irrigation diversions, siphons, and canals, which begin near Malheur river mile 65, near Namorf and Harper, Oregon.
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