Feature Name | Class | Elev. meters | County | Latitude DMS | Longitude DMS |
| Summerton Bog State Natural Area | Park | 44 | Marquette | 43 44 59 N | 089 31 28 W |
| Tamarack Creek Bog State Natural Area | Park | 44 | Trempealeau | 44 09 12 N | 091 26 56 W |
| Trempealeau Mountain State Natural Area | Park | 44 | Trempealeau | 44 01 17 N | 091 29 46 W |
| Trempealeau River Meadow State Natural Area | Park | 44 | Buffalo | 44 11 04 N | 091 36 26 W |
| Two Creek Buried Forest State Natural Area | Park | 44 | Manitowoc | 44 19 34 N | 087 32 41 W |
| Upper Fox Headwaters State Natural Area | Park | 44 | Marquette | 43 58 49 N | 089 29 30 W |
| Vanderbloemen Bog State Natural Area | Park | 44 | Manitowoc | 43 59 23 N | 087 53 59 W |
| Washburn Marsh State Natural Area | Park | 44 | Jackson | 44 14 38 N | 090 38 04 W |
| Waupun Park Maple Forest State Natural Area | Park | 44 | Fond du Lac | 43 38 45 N | 088 45 07 W |
| White River Prairie-Tamaracks State Natural Area | Park | 44 | Green Lake | 43 57 43 N | 089 09 15 W |
| White River Sedge Meadow State Natural Area | Park | 44 | Green Lake | 43 55 15 N | 089 06 17 W |
| Whitman Bottoms Floodplain Forest State Natural Area | Park | 44 | Buffalo | 44 09 58 N | 091 47 57 W |
| Wilderness Ridge State Natural Area | Park | 44 | Manitowoc | 44 12 32 N | 087 30 44 W |
| Woodland Dunes State Natural Area | Park | 44 | Manitowoc | 44 08 32 N | 087 36 32 W |
| Yellow River Oxbows State Natural Area | Park | 44 | Juneau | 43 58 35 N | 090 02 56 W |
| Ames Private Airport | Airport | 43 | Walworth | 42 39 04 N | 088 44 45 W |
| Audubon Goose Pond State Natural Area | Park | 43 | Columbia | 43 19 08 N | 089 21 58 W |
| Battle Bluff Prairie State Natural Area | Park | 43 | Vernon | 43 27 23 N | 091 12 02 W |
| Berger School (historical) | School | 43 | Richland | 43 20 41 N | 090 28 46 W |
| Cherry Lake Sedge Meadow State Natural Area | Park | 43 | Racine | 42 43 34 N | 088 14 33 W |
| Concord Church (historical) | Church | 43 | Richland | 43 27 56 N | 090 13 38 W |
| Dekorra Lutheran Cemetery | Cemetery | 43 | Columbia | 43 23 14 N | 089 32 20 W |
| Eagle Centre Prairie State Natural Area | Park | 43 | Waukesha | 42 52 19 N | 088 28 50 W |
| Eagle Oak Opening State Natural Area | Park | 43 | Waukesha | 42 51 59 N | 088 32 01 W |
| Edgewood Fruit Farm (historical) | Locale | 43 | Richland | 43 27 11 N | 090 31 49 W |
| Eiffmeyer Cemetery | Cemetery | 43 | Sauk | 43 24 26 N | 090 07 35 W |
| Elm Grove School (historical) | School | 43 | Richland | 43 16 28 N | 090 21 36 W |
| Evangel Baptist School | School | 43 | Milwaukee | 43 01 06 N | 087 55 11 W |
| Evangelical Cemetery | Cemetery | 43 | Columbia | 43 19 23 N | 089 23 31 W |
| Evangelical Cemetery | Cemetery | 43 | Columbia | 43 25 13 N | 089 34 55 W |
| Evangelical Lutheran Church of the Atomement | Church | 43 | Milwaukee | 43 06 24 N | 087 57 58 W |
| Gibraltar Rock State Natural Area | Park | 43 | Columbia | 43 20 33 N | 089 35 53 W |
| Groom School (historical) | School | 43 | Grant | 42 44 16 N | 090 56 18 W |
| Harris School (historical) | School | 43 | Sauk | 43 27 08 N | 090 08 49 W |
| Hogback Prairie State Natural Area | Park | 43 | Crawford | 43 12 19 N | 090 52 11 W |
| Jackson Marsh State Natural Area | Park | 43 | Washington | 43 20 21 N | 088 06 48 W |
| Karcher Springs State Natural Area | Park | 43 | Racine | 42 36 44 N | 088 15 06 W |
| Lake Shangri La and Benet Lake 1 | Reservoir | 43 | Kenosha | 42 30 24 N | 088 03 54 W |
| Limery Ridge Savanna State Natural Area | Park | 43 | Crawford | 43 04 49 N | 091 07 36 W |
| Lost Lake State Natural Area | Park | 43 | Columbia | 43 28 43 N | 089 31 55 W |
| Lower and Upper Phantom Lakes 60 | Reservoir | 43 | Waukesha | 42 51 24 N | 088 19 48 W |
| Northridge Lakes 1 and 2 | Reservoir | 43 | Milwaukee | 43 10 30 N | 087 59 48 W |
| Renak-Polak Maple-Beech Woods State Natural Area | Park | 43 | Racine | 42 48 20 N | 087 51 44 W |
| Rigdon Private Airport | Airport | 43 | Grant | 42 31 27 N | 090 35 27 W |
| Rocky Run Oak Savanna State Natural Area | Park | 43 | Columbia | 43 27 24 N | 089 20 33 W |
| Rush Creek State Natural Area | Park | 43 | Crawford | 43 22 47 N | 091 08 10 W |
| Sander's Park Hardwoods State Natural Area | Park | 43 | Racine | 42 41 26 N | 087 50 24 W |
| Scuppernong Prairie State Natural Area | Park | 43 | Waukesha | 42 54 05 N | 088 30 46 W |
| Sugar Creek Bluff State Natural Area | Park | 43 | Crawford | 43 20 47 N | 091 04 41 W |
| Tichigan and Buena Lakes 359 | Reservoir | 43 | Racine | 42 45 54 N | 088 12 48 W |
| Wauzeka Bottoms State Natural Area | Park | 43 | Crawford | 43 04 60 N | 090 51 37 W |
| Ableman's Gorge State Natural Area | Park | | Sauk | 43 29 18 N | 089 55 19 W |
| Abraham Coulee | Valley | | Trempealeau | 44 08 20 N | 091 21 03 W |
| Adams Creek | Stream | | Trempealeau | 44 34 26 N | 091 28 08 W |
| Adams Valley | Valley | | La Crosse | 43 55 03 N | 091 01 08 W |
| Ahnapee River | Stream | | Kewaunee | 44 36 30 N | 087 25 59 W |
| Alcohol Creek | Stream | | Price | 45 24 41 N | 090 15 58 W |
| Alder Creek | Stream | | Chippewa | 44 52 54 N | 091 08 55 W |
| Alder Creek | Stream | | Iron | 46 23 12 N | 090 24 56 W |
| Alder Creek | Stream | | Rusk | 45 19 39 N | 090 58 24 W |
| Alder Creek | Stream | | Rusk | 45 28 50 N | 091 16 28 W |
| Alder Creek | Stream | | Sawyer | 45 47 42 N | 091 22 40 W |
| Alder Creek | Stream | | Winnebago | 44 10 19 N | 088 50 43 W |
| Alery Creek | Stream | | Lincoln | 45 19 39 N | 089 46 32 W |
| Allen Creek | Stream | | Forest | 46 01 05 N | 088 42 15 W |
| Allen Creek | Stream | | Green | 42 44 28 N | 089 26 25 W |
| Allen Creek | Stream | | Jackson | 44 19 23 N | 090 49 57 W |
| Allen Creek | Stream | | Jefferson | 42 54 09 N | 088 52 01 W |
| Allen Creek | Stream | | Marquette | 43 45 02 N | 089 28 38 W |
| Allen Creek | Stream | | Monroe | 43 58 39 N | 090 20 30 W |
| Allen Creek | Stream | | Waupaca | 44 19 34 N | 089 12 06 W |
| Allenton Creek | Stream | | Washington | 43 23 50 N | 088 19 37 W |
| Allequash Creek | Stream | | Vilas | 46 02 18 N | 089 36 51 W |
| Alto Creek | Stream | | Dodge | 43 35 10 N | 088 53 38 W |
| Alvin Creek | Stream | | Forest | 45 58 52 N | 088 52 14 W |
| Amacher Hollow | Valley | | Iowa | 43 06 54 N | 089 58 11 W |
| American Valley | Valley | | Trempealeau | 44 15 17 N | 091 30 18 W |
| Ames Branch | Stream | | Lafayette | 42 39 27 N | 090 04 49 W |
| Amnicon River | Stream | | Douglas | 46 41 31 N | 091 51 30 W |
| Amo Creek | Stream | | Jackson | 44 24 02 N | 090 56 34 W |
| Anderson Coulee | Valley | | La Crosse | 43 58 09 N | 090 58 10 W |
| Anderson Creek | Stream | | Douglas | 46 40 26 N | 091 43 03 W |
| Anderson Creek | Stream | | Fond du Lac | 43 49 45 N | 088 27 53 W |
| Anderson Valley | Valley | | Eau Claire | 44 39 13 N | 091 25 09 W |
| Angelo Lake Creek | Stream | | Oneida | 45 40 01 N | 089 16 23 W |
| Annis Creek | Stream | | Dunn | 44 55 33 N | 091 59 14 W |
| Antigo Air Force Station (historical) | Military (Historical) | | Langlade | 45 02 57 N | 089 14 04 W |
| Apple Branch | Stream | | Lafayette | 42 40 38 N | 089 54 09 W |
| Apple Creek | Stream | | Brown | 44 21 20 N | 088 08 42 W |
| Apple Creek | Stream | | Iron | 46 21 08 N | 090 24 18 W |
| Apple Creek | Stream | | Monroe | 44 07 52 N | 090 28 34 W |
| Apple River | Stream | | St. Croix | 45 08 52 N | 092 44 53 W |
| Arcade Glen | Valley | | Fond du Lac | 43 51 09 N | 088 52 09 W |
| Argus School Branch | Stream | | Green | 42 39 26 N | 089 39 58 W |
| Arkansaw Creek | Stream | | Pepin | 44 37 32 N | 092 00 46 W |
| Armour Valley | Valley | | Buffalo | 44 33 44 N | 091 38 53 W |
| Armstrong Creek | Stream | | Forest | 45 33 33 N | 088 29 20 W |
| Armstrong Creek | Stream | | Lincoln | 45 26 48 N | 089 51 14 W |
| Arneson Creek | Stream | | Iowa | 43 02 52 N | 089 56 47 W |
| Arnold Creek | Stream | | Clark | 44 25 24 N | 090 43 15 W |
| Arnold Creek | Stream | | Douglas | 46 15 26 N | 091 57 49 W |
| Arrow Branch | Stream | | Grant | 42 43 45 N | 090 45 11 W |
| Arrowhead River | Stream | | Winnebago | 44 08 31 N | 088 42 09 W |
| Artist Glen | Valley | | Adams | 43 39 11 N | 089 47 06 W |
| Artus Creek | Stream | | Marathon | 44 56 18 N | 089 47 59 W |
| Ash Creek | Stream | | Richland | 43 17 14 N | 090 19 52 W |
| Ashippun River | Stream | | Waukesha | 43 10 14 N | 088 33 14 W |
| Ashwaubenon Creek | Stream | | Brown | 44 28 09 N | 088 03 23 W |
| Auburn Lake Creek | Stream | | Fond du Lac | 43 34 45 N | 088 14 17 W |
| Augustine Creek | Stream | | Ashland | 46 08 34 N | 090 26 56 W |