| Wood Duck Pond | Canyon, ID | 9.6 miles | NE |
| Pintail Pond | Canyon, ID | 9.9 miles | NE |
| Ralphs Pond | Canyon, ID | 10 miles | NE |
| Redhead Pond | Canyon, ID | 10.2 miles | NE |
| Swan Pond | Canyon, ID | 10.3 miles | NE |
| Dry Lake | Malheur, OR | 12.5 miles | SW |
| Freezeout Lake | Malheur, OR | 21.5 miles | SW |
| Cottle Lake | Owyhee, ID | 32.2 miles | SE |
| Tule Lake | Malheur, OR | 32.7 miles | SW |
| Jensen Lake | Canyon, ID | 35 miles | SE |
| Hole in the Rock | Malheur, OR | 38.4 miles | SW |
| Wildcat Waterhole | Malheur, OR | 38.6 miles | NW |
| Halverson Lake | Ada, ID | 38.7 miles | SE |
| Lake Elmore | Ada, ID | 39.3 miles | SE |
| Boise Cascade Lake | Ada, ID | 41.2 miles | SE |
| Johnston Lakes | Owyhee, ID | 41.4 miles | SE |
| Siphon Lakes | Boise, ID | 42.1 miles | NE |
| Home Lake | Boise, ID | 42.6 miles | NE |
| Batch Lake | Malheur, OR | 44.6 miles | SW |
| Lower Batch Lake | Malheur, OR | 45.2 miles | SW |
| Tex Martin Lake | Malheur, OR | 48.2 miles | SW |
| Bogus Lake | Malheur, OR | 50.4 miles | SW |
| Karney Lakes | Boise, ID | 50.4 miles | SE |
| Bull Creek Pond | Malheur, OR | 50.7 miles | NW |
| Creston Waterhole | Malheur, OR | 50.7 miles | SW |
| Westfield Pit | Malheur, OR | 50.9 miles | SW |
| Mud Lake | Malheur, OR | 51.1 miles | SW |
| Thomas Lakes | Owyhee, ID | 51.4 miles | SE |
| Lone Pine Lake | Boise, ID | 54.5 miles | NE |
| Beech Lake | Gem, ID | 55.7 miles | NE |
| Tadpole Lake | Ada, ID | 55.8 miles | SE |
| Mud Lake | Boise, ID | 55.8 miles | NE |
| Y Reservoir | Baker, OR | 56 miles | NW |
| Williams Charco | Malheur, OR | 56.1 miles | SW |
| Wind Butte Lakes | Ada, ID | 56.8 miles | SE |
| Juniper Mountain Waterhole Number Two | Baker, OR | 56.9 miles | NW |
| Lake Bed Waterhole | Malheur, OR | 57.5 miles | SW |
| Dry Lake | Malheur, OR | 60.4 miles | NW |
| Mouse Lake | Malheur, OR | 62 miles | NW |
| Head of the Creek Waterhole | Malheur, OR | 62.3 miles | SW |
| Hat Butte Waterhole | Malheur, OR | 63 miles | SW |
| Lakebed Waterhole | Malheur, OR | 63.1 miles | SW |
| Newts Waterhole | Malheur, OR | 63.7 miles | SW |
| Soda Lake | Baker, OR | 66.4 miles | NW |
| Woodroad Waterhole | Harney, OR | 66.5 miles | SW |
| Floater Waterhole | Harney, OR | 67.5 miles | SW |
| Top of the Hill Waterhole | Harney, OR | 67.9 miles | SW |
| Blue Lake | Valley, ID | 68.4 miles | NE |
| Gabes Bathtub | Gem, ID | 68.5 miles | NE |
| Coyote Waterhole | Baker, OR | 68.5 miles | NW |
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