Source: Fishing in Oregon: The Complete Oregon Fishing Guide (11th Edition) by Madelynne Diness Sheehan
The Southeast Zone includes all tributaries (including impoundments) of the Snake River system above Hells Canyon Dam; the Silvies River drainage in Grant County; all waters in the Malheur and Lake counties; all waters in Harney County except the drainage of the South Fork of the John Day River; and all waters of the Klamath River Basin in Klamath and Lake counties.
(The Klamath River Basin is where all streams and their tributaries drain toward Upper Klamath Lake or the Klamath River.) This zone does not include any portion of the mainstem Snake River.
The following are among the best fishing rivers (outside the Klamath Basin) in the Southeast Zone:
Donner Und Blitzen (Blitzen) River
Often simply called the Blitzen, this river in the Frenchglen area offers quality fishing for redband rainbow trout in rugged and remote country south of Burns. The Blitzen can be very turbid during spring run-off.
Though the river can be productive from mid- to late summer, it gets hot here. Fall fishing is pleasant. Fishing is restricted to artificial flies and lures. Be on the watch for rattlesnakes, and come prepared with water, spare tires and emergency supplies.
The river features abundant large trout, but only when sufficient water supplies allow stable flows out of Beulah and Warm Springs reservoirs.
There are more hatchery rainbows at the upstream end of the mainstem, below the junction of the Middle and South forks near Riverside, including some really large escapees that move downstream from the reservoirs.
Downstream from Juntura, there are increasingly more non-trout species in the mix, but trout can be caught down to about Gold Creek. There are mostly catfish in the stream by the time it reaches Vale and Ontario and enters the Snake River at the Idaho border.
Malheur River, Middle Fork
This productive river for wild redband trout and smallmouth bass is one of the state’s best-kept angling secrets. It is marked simply as the Malheur River on the most popular map. The upper Middle Fork is no longer stocked but has excellent numbers of wild rainbows up to 16 and 18 inches.
Whitefish are in the stream, as well as brook trout in the upper reach. Bull trout must be released unharmed. South of Highway 20 there is excellent smallmouth bass fishing as long as water conditions have been good for a few years.
Below Warm Springs Reservoir, the Middle Fork Malheur offers an excellent tailrace fishery for trout to 20 inches when water supplies are high enough to augment the flow.
This river south of Ontario has two sides: A very good tailrace fishery for large redband rainbow and brown trout in the river below Owyhee Reservoir and some good smallmouth bass and channel catfish angling above the huge impoundment.
The first 13 miles below Owyhee Dam are the best trout water, particularly from mid-October through mid-April, when there is no great fluctuation from irrigation withdrawals. Rainbows averaging 12 to 14 inches (and up to 6 pounds) are most often caught in riffles.
Browns are commonly caught in the 4- to 6-pound range (and up to 12 pounds), mostly in pools. The upper river is more famous for whitewater rafting but offers excellent smallmouth bass fishing. Catfish are most abundant from Rome down to the reservoir.
For more info, read Owyhee River Fly Fishing for Trout.