Rising in Big Cow Burn in the Blue Mountains, it flows generally south to join the larger river at Juntura.

This part of the river basin offers camping, hiking, and fishing opportunities in a remote forest setting.

Dugout Creek enters from the left before the river passes under a footbridge carrying a hiking trail running parallel to the stream.

[7] As it leaves the reservoir, the river passes a stream gauge at Beulah, 14.5 miles (23.3 km) from the mouth.

[8] The United States Geological Survey monitors the flow of the North Fork Malheur River.

The maximum flow recorded there was 7,000 cubic feet per second (198 m3/s) on May 7, 1942, during a flood caused by failure of the gates at Agency Valley Dam.

These include a parking lot, boat ramp, and restroom, all near the dam, 15 miles (24 km) north of Juntura on a gravel road.

[11] Fishing is limited to artificial flies and lures,[11] and bull trout, which are threatened,[9] must be released unharmed.