| June 1998 | Thunderstorm Wind | West Salem | 13 hurt, $20,000 | Circus tent collapsed at fairgrounds. 500 people were in tent. 13 injured. |
| May 1965 | Tornado (F3) | not stated | 1 hurt, $2,500,000 | no account filed |
| May 1998 | Tornado (F0) | West Salem | 1 hurt, $40,000 | no account filed |
| July 1966 | Tornado (F1) | not stated | 1 hurt, $25,000 | no account filed |
| July 2003 | Thunderstorm Wind | La Crosse | 1 hurt, $2,750 | no account filed |
| June 2020 | Hail | Holmen | $45,500,000 | Hail ranging in size from 1 inch upto 2.5 inches in diameter fell in Holmen. Most of the hail was golf ball sized or larger. Between 4,000 and 5,000 homes sustained roof damage from the hail. |
| April 2011 | Hail | Calvert | $20,000,000 | Hundreds of homes received roof and siding damage as well as broken windows on the south side of La Crosse. Wal Mart department store reported approximately 20 sky lights broken. Hundreds of cars were also damaged with dents and broken windows and mirrors. There were several thousand claims made to major insurance companies in and around the La Crosse area. |
| May 2011 | Tornado (EF2) | La Crosse | $15,200,000 | This tornado originally began in Houston County Minnesota and crossed into La Crosse near Target Lake. The first damage occurred on Green Island where numerous mature trees were snapped off and substantial damage occurred to the Green Island ice arena. The tornado then moved into a residential area where buildings sustained partial roof removal and garages were heavily damaged. Buildings in a small industrial area near the intersection of Green Bay Street and West Ave had walls partially collapse causing the roofs to subsequently collapse and a small apartment complex had its roof cleanly removed. After this, the tornado tracked primarily through residential areas until it dissipated causing mainly tree damage and light structural damage to homes and garages. An estimated 200 homes and businesses were damaged, 9 homes were destroyed and another 6 buildings condemned and uninhabitable. An emergency shelter was set up where up to 40 people sought refuge at times with 14 spending the night. This tornado was the first to hit the city of La Crosse since 1966 when a tornado moved across the airport. Total damages were estimated to be just over $15 million. An estimated 6,300 customers lost power as a result of the tornado. There was not a single ambulance call right after the tornado, but some did occur during the following days during clean up. |
| August 2007 | Flash Flood | La Crosse | $11,900,000 | Heavy rain led to major flash flooding in the south end of the county, especially south of La Crosse. Mudslides were reported along Highways 35 and 33. There was also major street flooding and water in basements. Parts of a retaining wall washed away at the intersection of Highways 14, 61, and 35 and erosion washed away some smaller roads.||About 644 people applied for FEMA assistance. |
| April 2011 | Hail | Calvert | $5,000,000 | no account filed |
| July 2017 | Flash Flood | Stevenstown | $2,600,000 | Heavy rains, with totals of 6 to 8 inches, produced flash flooding across La Crosse County. The Shelby Fire Department had to evacuate people along County Road M in the township of Greenfield. Some of these evacuations had to be made by boat. Other rescues had to be made along Kammell Coulee Road southeast of St. Joseph. County Road U was closed between Bangor and Rockland due to flooding along Fish Creek. Flood waters along Mormon Creek washed out the approaches to both sides of a bridge on Breidel Coulee Road south of Barre Mills. Some streets in Onalaska were washed out or completely underwater. Numerous streets in the city of La Crosse were underwater causing a giant sinkhole to form near Myrick Park. Every state and county highway, with the exception of Interstate 90 and U.S. Highway 53, sustained some damage. At least 60 township roads across the county were closed or impacted by flood waters. In Bangor, flood waters from Dutch Creek washed away the pedestrian walking bridge in Veterans Memorial Park. Boats on Lake Neshonoc broke loose from their moorings and became lodged against the dam. All the trails in the Hixton Forest suffered erosion damage that caused holes and blowouts to form. The damage to the trails caused a mountain bike race course to be limited to trails that stayed on top of the bluffs. A bike trail along Halfway Creek near Holmen was washed out in several places with other damage caused by logjams and debris in the water. |
| July 2017 | Flood | Stevenstown | $2,300,000 | After the initial round of flash flooding, the flood waters continued to cause problems into Friday, July 21st. Numerous roads across the county remained closed until the flood waters receded. |
| June 2020 | Hail | New Amsterdam | $2,100,000 | Hail up to 2.5 inches in diameter fell in New Amsterdam. |
| August 2007 | Flash Flood | La Crosse | $1,300,000 | Up to 200 people were evacuated at Goose Island camp ground due to flash flooding and a nearby train derailment. The train derailment was due to mud and debris across the railroad tracks. |
| September 2016 | Flash Flood | Rockland | $913,000 | Flood waters from Fleming Creek caused State Highway 108 to be closed near Mindoro.|Water covered low spots in several other locations across the northeast part of La Crosse County. Some of the impacted roads included County Highways C, DE and E. Some minor mudslides also occurred with County Highway OA reduced to one lane. Sixteen homes were damaged by the flooding. Bangor declared a local state of emergency due to flooding along Dutch Creek. |
| August 2018 | Flash Flood | Calvert | $650,000 | Runoff from heavy rain caused flash flooding across the southern portions of La Crosse County. Homes were evacuated and roads closed along State Highway 35 south of La Crosse and County Road K near Goose Island Park. Flood waters from Mormon Creek were chest high in a mobile home part along U.S. Highways 14/61 southeast of La Crosse where water rescues had to be performed. The BNSF rail line was closed because of washouts between La Crosse and the Vernon County line. Sections of Highways 14/61 in the southern end of the county were damaged and had mudslides over them. |
| July 2024 | Flood | La Crosse | $540,000 | Significant rainfall throughout June pushed the Mississippi River at La Crosse into flood stage in June and continued into July. The river stage crested during the evening on July 2nd in moderate flood stage at 14.94 ft. |
| June 2007 | Hail | Bangor | $500,000 | no account filed |
| May 2022 | Hail | Holmen | $405,000 | Up to golf ball sized hail fell in Holmen. |
| June 2008 | Flood | La Crosse | $400,000 | Heavy rains led to flooding over parts of the county, especially the southern tier where ponding of water flooded some basements and damaged secondary roads. About 60 residents applied for FEMA assistance. |
| August 2007 | Flood | La Crosse | $400,000 | Flooding continued along many creeks, streams and rivers. Law enforcement officials reported numerous roads and bridges were either washed out or still under water. All or portions of highways still closed included Highway 35 south of La Crosse and County Road GI to Goose Island Park. |
| August 2018 | Flash Flood | La Crosse | $375,000 | Runoff from heavy rains produced street flooding in various locations around the city of La Crosse. Travel in the city was severely impacted, water flowed into people's yards and lawns, and some cars became stranded in deeper intersections. |
| July 2004 | Hail | La Crosse | $350,000 | no account filed |
| July 2004 | Hail | La Crosse | $320,000 | no account filed |
| March 2017 | Tornado (EF1) | West Salem Arpt | $290,000 | The tornado started just north of Barre Mills and rapidly moved northeast before dissipating south of West Salem. A broken damage path was found by the survey team. Along the path, the tornado snapped numerous trees, destroyed some small farm buildings, a silo, parts of several barns, removed part of the roof from one house, heavily damaged another and damaged the porch on a farm house. There was other damage along Interstate 90 that may have been related to this tornado. |
| September 2024 | Hail | Holmen | $254,000 | The public reported two inch diameter hail near Holmen. |
| May 2017 | Lightning | Holmen | $250,000 | A fire at a care facility in Holmen was started by a lightning strike. The fire was trapped between the ceiling and roof with the building sustaining substantial water and fire damage. All the residents of the care facility were safely evacuated. |
| June 2008 | Heavy Rain | (Lse)La Crosse Muni | $250,000 | Total rainfall for the weekend (June 7-8) was 4.40 inches at the La Crosse Mun. Airport. An amateur radio operator in La Crosse had 3.49 inches. |
| June 1981 | Tornado (F1) | not stated | $250,000 | no account filed |
| June 1980 | Tornado (F2) | not stated | $250,000 | no account filed |
| June 1998 | Thunderstorm Wind | La Crosse | $200,000 | no account filed |
| July 1995 | Thunderstorm Wind | La Crosse | $200,000 | no account filed |
| April 2013 | Hail | La Crosse | $170,000 | Quarter sized hail fell on the south side of the city of La Crosse. This hail created minor dings on almost 170 vehicles at a car dealership. |
| September 2010 | Flood | Council Bay | $170,000 | Several roads were closed in the northern part of the county due to water over the roads. County Road C was closed between County Roads DE and T, while 5 inches of water sat on the road at the intersection of County Roads C and DE. Other roads over-topped with water included Herman Coulee Road, portions of State Highway 162 and County Road A. There was also minor damage to 2 homes and 1 business from flood waters. In the two hours between 5:30 p.m. and 7:30 p.m. CST on the 22nd, the rainfall amounted to 1.15 inches, with widespread storm total amounts through the evening of the 23rd of 3.30 to 4.00 inches. |
| July 2013 | Hail | Medary | $150,000 | Large spiky hail, estimated to be in excess of 2.5 inches in diameter, fell along Interstate 90 in Onalaska. Vehicles at two car dealerships were damaged by the hail. |
| July 1999 | Thunderstorm Wind | Barre Mills | $150,000 | no account filed |
| July 2023 | Thunderstorm Wind | Bangor | $100,000 | Public reported tree fallen upon house in Bangor. |
| June 2007 | Hail | West Salem | $100,000 | Large hail damaged cars and homes. |
| June 2007 | Hail | West Salem | $100,000 | no account filed |
| June 2008 | Tornado (EF1) | Barre Mills | $93,000 | A tornado occurred at 5:45 p.m. CDT in La Crosse County, WI, near Barre Mills and it was surveyed by a National Weather Service meteorologist on Sunday, June 8th. The tornado initially touched down just west of Russian Coulee Road approximately two miles east of Barre Mills (La Crosse County). There the tornado destroyed one metal barn and partially unroofed another. Much of the debris from the first barn was thrown to the north; however, some of its debris was scattered to the east for nearly a half mile up a hill. A family of five heard the tornado and they took cover in a basement. Fortunately no one was injured.||The tornado then proceeded over a hill and moved through another farmstead. It destroyed a barn and unroofed much of the adjacent house. Both soft and hardwood trees were either snapped or uprooted. ||The tornado then moved through several wooded areas as it crossed County Road II, Antony Road, County Road II again, and then Highway 162 near Souchek Road.||The path of this tornado was about 6 miles long with an average width of 600 feet. It has an EF1 rating (estimated wind speeds of 90 to 110 mph). Several nearby neighbors saw the tornado as it moved through both farmsteads. |
| August 2010 | Flood | Herrington | $90,000 | Street flooding occurred in parts of the city of La Crosse after heavy rains fell during the morning hours. Flooding along Diagonal Road caused a house foundation to collapse filling the basement with mud. The house was later condemned and razed. Losey Avenue near Main Street was under water temporarily. The automated weather observing equipment at the La Crosse Airport recorded 1.65 inches of rainfall in one hour, ending at 0453 CST, while 2.11 inches fell in the two hours between 0341 CST and 0541 CST. Also, 2.21 inches of rain was observed at the La Crosse National Weather Service office between the hours of 0324 CST and 0533 CST. |
| July 1999 | Thunderstorm Wind | La Crosse | $85,000 | no account filed |
| December 2021 | Thunderstorm Wind | Lytle | $80,000 | A path of wind damage occurred just west of Holmen. A barn was destroyed, the wall ripped off another barn, metal roofing removed from an outbuilding, a large sign on three steel I-beams was flattened and numerous trees were snapped off or uprooted. |
| August 2021 | Flood | (Lse)La Crosse Muni | $75,000 | Following the heavy rains of August 7th, runoff from more rain on the 8th caused flooding to occur on the west side of French Island in the Town of Campbell. The basement wall on one house collapsed allowing water to fill the basement and prompted the evacuation of the residents. |
| December 2021 | Thunderstorm Wind | La Crosse | $75,000 | Two temporary structures for the Rotary Lights display in La Crosse were destroyed. |
| June 2006 | Lightning | La Crosse | $75,000 | no account filed |
| May 2017 | Thunderstorm Wind | West Salem | $70,000 | A path of straight line wind damage was found from the east of Lake Neshonoc to northwest of Bangor. Approximately 250 trees were damaged or uprooted, a barn was destroyed, another barn lost part of its roof and there was minor damage to a house and garage. |
| August 2016 | Lightning | West Salem Arpt | $70,000 | A lightning strike started a house fire west of West Salem. The garage and front half of the house were badly burned while the rest of the structure sustained water and smoke damage. |
| July 2023 | Hail | Neshbonoc Lake | $65,000 | Public reported softball sized hail near Neshbonoc Lake via Social Media picture. |
| July 2023 | Hail | West Salem | $65,000 | Public reported tennis ball sized hail and broken windows in West Salem. |
| June 2011 | Flood | Onalaska | $65,000 | A house that was built on a sunken lot had a basement wall collapse after four inches of rain fell on the area. In addition to the basement damage, the master bedroom and bathroom, laundry room and living room were ruined. |
| July 2015 | Lightning | Calvert | $60,000 | Lightning struck a tree located between two homes on the south side of the city of La Crosse. Fires started in both homes from the lightning strike with moderate damage reported. Several other homes sustained damage to their gas meters. |
| March 2019 | Flood | Burr Oak | $55,000 | Runoff from melting snow caused flooding to occur along numerous streams across La Crosse County. Numerous county and town roads were closed because of the flooding and some homes were evacuated in the Holmen area. Around 65 homes were affected by the flooding. |
| July 2023 | Hail | Bangor | $50,000 | Public reported baseball sized hail near Bangor. |
| July 2023 | Hail | West Salem | $50,000 | Law enforcement reported baseball hail near West Salem. |
| July 2023 | Hail | West Salem | $50,000 | Public reported tea cup sized hail near West Salem via picture. |
| July 2022 | Thunderstorm Wind | La Crosse | $50,000 | Several large trees were blown down across and near La Crosse. Some of the downed trees caused damage to homes and buildings. |
| June 2014 | Thunderstorm Wind | (Lse)La Crosse Muni | $50,000 | An industrial warehouse near the La Crosse airport suffered wind damage with the debris spread across a parking lot and onto the airfield. |
| June 2007 | Hail | Bangor | $50,000 | no account filed |
| June 2007 | Hail | West Salem | $50,000 | no account filed |