The Wallowa River begins in the Eagle Cap Wilderness and flows into Wallowa Lake. The river above Wallowa Lake is fun to fly fish for Rainbow and Eastern Brook Trout. The West Fork mostly contains Rainbow Trout, while the East Fork contains Eastern Brook Trout.
It's hard to imagine, but there are over 50 lakes in the Eagle Cap Wilderness, many of them with good populations of Rainbow and Brook Trout. The hard part, of course, is hike it requires to get there. The area with the greatest concentration of open water is the Lakes Basin. It's central and reachable from almost all the trail heads in the area with the Lostine River/Two Pan Trail Head providing the closest (and most popular) access. Fishing is an awesome experience in this absolutely gorgeous area.
The Imnaha River is a designated a 'Wild and Scenic' river and is a tributary to the mighty Snake River. The river starts in the Eagle Cap wilderness and eventually flows into the Snake River some 60 miles later. The section of the river known as the Upper Imnaha flows along the southern boarder of the Hells Canyon National Recreation Area.
The Grande Ronde River has excellent opportunities to catch Rainbow Trout above Boggan’s Oasis and Smallmouth Bass in the section below. In addition, there is steelhead fishing throughout the river starting October 15 until the spring thaw (March).
All around the county are small ponds that are stocked at least once in the summer. While these might not appeal to the 'serious' fisherman, they provide a great opportunity for younger or beginning fisherman to learn and have fun. Marr, Kinney, Salt Creek Summit, McGraw, Honeymoon and Tee Pee Ponds are usually date-posted on the OFDW stocking page so you can figure when to get there.