| Bogus Lake | Malheur, OR | 10.4 miles | NW |
| Lower Batch Lake | Malheur, OR | 11.7 miles | NE |
| Batch Lake | Malheur, OR | 12.2 miles | NE |
| Long Water Holes | Malheur, OR | 20.8 miles | SW |
| Mustang Water Hole | Malheur, OR | 23.7 miles | SE |
| Deadman Water Hole | Malheur, OR | 24.2 miles | SW |
| Tule Lake | Malheur, OR | 24.9 miles | NE |
| Mud Lake | Malheur, OR | 27.9 miles | NW |
| Tex Martin Lake | Malheur, OR | 31.8 miles | NW |
| Peacock Lake | Malheur, OR | 32 miles | SW |
| Johnston Lakes | Owyhee, ID | 35.1 miles | NE |
| Heath Lake | Harney, OR | 39.8 miles | NW |
| Cottle Lake | Owyhee, ID | 39.9 miles | NE |
| Hole in the Rock | Malheur, OR | 40.2 miles | NW |
| Ten Cent Lake | Harney, OR | 41 miles | NW |
| Lakebed Waterhole | Malheur, OR | 42.1 miles | NW |
| Thomas Lakes | Owyhee, ID | 42.1 miles | NE |
| Hat Butte Waterhole | Malheur, OR | 43.2 miles | NW |
| Newts Waterhole | Malheur, OR | 43.3 miles | NW |
| Head of the Creek Waterhole | Malheur, OR | 43.6 miles | NW |
| Juniper Lake | Harney, OR | 43.6 miles | NW |
| Tudor Lake | Harney, OR | 44.8 miles | SW |
| Bull Flat Lake | Malheur, OR | 44.9 miles | SE |
| Squaw Lake | Harney, OR | 45.3 miles | NW |
| South Fork Waterhole | Harney, OR | 45.7 miles | NW |
| Comegys Lake | Harney, OR | 46.3 miles | NW |
| Woodroad Waterhole | Harney, OR | 46.5 miles | NW |
| Dry Lake | Malheur, OR | 47.2 miles | NE |
| Floater Waterhole | Harney, OR | 47.2 miles | NW |
| Oregon Lake | Malheur, OR | 47.7 miles | SE |
| Top of the Hill Waterhole | Harney, OR | 48.1 miles | NW |
| Three Lakes | Harney, OR | 48.9 miles | NW |
| Mann Lake | Harney, OR | 49.9 miles | SW |
| Dollar Lake | Harney, OR | 50.3 miles | SW |
| Freezeout Lake | Malheur, OR | 50.3 miles | NW |
| Westfield Pit | Malheur, OR | 50.4 miles | NW |
| Creston Waterhole | Malheur, OR | 51.4 miles | NW |
| Deep Hole | Harney, OR | 51.6 miles | NW |
| Hole in the Ground | Harney, OR | 51.8 miles | NW |
| Indian Lake | Owyhee, ID | 52.2 miles | SE |
| Sheep Creek Pond | Owyhee, ID | 52.8 miles | SE |
| Jensen Lake | Canyon, ID | 54.5 miles | NE |
| Wildcat Waterhole | Malheur, OR | 55.6 miles | NW |
| Halverson Lake | Ada, ID | 56.1 miles | NE |
| Paws Water | Owyhee, ID | 57.6 miles | SE |
| Lookout Lake | Malheur, OR | 58.2 miles | SE |
| Road Lake | Harney, OR | 58.2 miles | NW |
| Ham Brown Lake | Harney, OR | 58.6 miles | SW |
| Kegler Lake | Harney, OR | 58.9 miles | NW |
| Wildhorse Lake | Harney, OR | 59.7 miles | SW |
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