There are hundreds of lakes in the Sawtooth Mountains, most of which have been created by alpine glaciers. The majority of the lakes are within the Sawtooth Wilderness, but several are not yet still within Sawtooth National Recreation Area The largest lakes are Redfish, Alturas, Pettit, Yellow Belly, Stanley, and Sawtooth lakes.[1]
| Alturas Lake | 43.9135°N -114.8606°W | Alturas Lake Creek | Blaine |
| Little Redfish Lake | 44.1586°N -114.9083°W | Redfish Lake Creek | Custer |
| Lower Hanson Lake | 44.2075°N -115.1137°W | Stanley Lake Creek | Custer |
| McDonald Lake | 43.998°N -114.8895°W | Yellow Belly Lake Creek | Custer |
| Middle Hanson Lake | 44.2094°N -115.117°W | Stanley Lake Creek | Custer |
| Perkins Lake | 43.9286°N -114.8404°W | Alturas Lake Creek | Blaine |
| Pettit Lake | 43.9793°N -114.8805°W | Pettit Lake Creek | Blaine |
| Redfish Lake | 44.1167°N -114.9333°W | Redfish Lake Creek | Custer |
| Stanley Lake | 44.2442°N -115.059°W | Stanley Lake Creek | Custer |
| Upper Hanson Lake | 44.2104°N -115.1231°W | Stanley Lake Creek | Custer |
| Yellow Belly Lake | 44.0008°N -114.8751°W | Yellow Belly Lake Creek | Custer |
| Bench Lakes5 | 44.117°N -114.9506°W | Redfish Lake Creek | Custer |
| Feather Lakes4 | 44.0674°N -115.0511°W | Goat Creek | Boise |
| McGown Lakes7 | 44.1853°N -115.0833°W | Stanley Lake Creek | Custer |
| Saddleback Lakes5 | 44.0639°N -114.972°W | Redfish Lake Creek | Custer |
| Stevens Lakes4 | 44.1086°N -115.0176°W | Fishhook Creek | Custer |
| Trail Creek Lakes5 | 44.1584°N -115.087°W | Trail Creek | Boise |
| Trailer Lakes3 | 44.1654°N -115.0729°W | Trail Creek | Boise |
| Twin Lakes2 | 43.9362°N -114.9554°W | Pettit Lake Creek | Blaine |
| Upper Redfish Lakes5 | 44.0461°N -115.0355°W | Redfish Lake Creek | Custer |