| August 2007 | Flash Flood | Lewiston | 5 killed, $300,000 | Five fatalities were reported from people driving into flood waters. Two fatalities occurred near Witoka when a couple's vehicle fell into a chasm along County Road 17 that had opened when flood waters washed out the road. Near Stockton, two fatalities occurred when a couple's vehicle was swept away by flood waters from Garvin Brook. Near the Enterprise rest area on Interstate 90, a man was killed when his vehicle was washed away by flood waters along Rush Creek. |
| May 1953 | Tornado (F4) | not stated | 5 hurt, $2,500,000 | no account filed |
| July 1999 | Tornado (F2) | Lewiston | 2 hurt, $2,000,000 | no account filed |
| July 2010 | Hail | Nodine | 1 hurt | A motorcycle passenger was hit on the head by hail on Interstate 90 near Nodine. The passenger was taken by ambulance to a hospital. |
| August 2007 | Flash Flood | Stockton | $22,000,000 | Flash flooding hit all the creeks and drainage areas hard that begin near the Interstate 90 area in Winona County. Garvin Brook and other creeks that flow into Stockton became terrain-changing flowages that washed out numerous roads, created massive mudslides, took out bridges, damaged railroad tracks, and washed away some homes.||Most homes in Stockton had severe water damage as flood waters roared through town.||Erosion problems were also noted south of Interstate 90 in the Hart area. Many roads, including Highway 43, were closed for several days. |
| August 2007 | Flash Flood | Winona | $12,000,000 | All drainage areas leading into communities in eastern Winona County experienced tremendous flash flooding. State Highway 43 was washed out just south of Winona. In addition, more than 300 residents were evacuated from their homes in Goodview due to high water. In Minnesota City a railroad bridge was ripped apart by Garvin Brook and a highway bridge through town suffered major damage on each end. Railroad tracks were warped or pushed clear out of position. Major erosion was seen. |
| August 2007 | Flash Flood | Lewiston | $6,000,000 | Flash flooding and mudslides were common from the Elba area through Whitewater State Park and into the Lewiston area. Numerous mudslides occurred with many roads closed. Debris slid down hills and blocked drainage areas making flooding worse in many areas. A car was stuck in high water on County Highway 29 at some point.||Highway 74 in Whitewater State Park completely washed out. About 500 campers were evacuated that evening, but about a dozen campers were stranded at a primitive campsite overnight. They were rescued the following morning. The state park lost 3 bridges and there was extreme damage to campgrounds, rest rooms, a group dining hall, and the septic and water systems totaling at least one million dollars. The flood system installed at the park did activate that evening.||Many area creeks and trout streams were heavily damaged. |
| June 2021 | Hail | Goodview | $3,000,000 | Baseball sized hail fell in Goodview. |
| May 1965 | Tornado (F3) | not stated | $2,500,000 | no account filed |
| June 2020 | Hail | Winona | $1,800,000 | Hail ranging in size from 1.25 to 2 inches in diameter moved across the city of Winona causing extensive roof damage to houses and buildings. |
| August 2007 | Flood | Winona | $1,500,000 | Law enforcement officials reported some roads and bridges washed out or still under water. Whitewater State Park remained closed. In Goodview, extensive damage occurred to homes and apartments due to flood waters. All or portions of highways still closed included Highway 76 from Interstate 90 to Highway 16. |
| September 2010 | Flood | Troy | $1,360,000 | Flooding occurred along rivers, creeks, and streams as well as in low-lying areas, with the worst impacts seen in the northern parts of the county. Numerous roads were closed and some were damaged by flood waters. A portion of County Road 74 southwest of Elba was closed due to high water. The Whitewater River saw major flooding, which did some damage to portions of the Whitewater State Park, which was evacuated. Five homes incurred minor damage. At mid-morning on the 23rd, the majority of the rain had fallen with 5.52 inches measured at a location 5 miles north of St. Charles and 4.20 inches in Winona. |
| June 2020 | Hail | Homer | $900,000 | Hail ranging in size from 1.25 to 2 inches in diameter fell from the south side of Winona to near Pickwick. |
| June 2021 | Hail | Goodview | $800,000 | Golf ball sized hail fell in Goodview. |
| June 1998 | Thunderstorm Wind | Winona | $400,000 | no account filed |
| June 1998 | Thunderstorm Wind | Winona Muni Arpt | $300,000 | no account filed |
| July 2023 | Hail | Bethany | $250,000 | Public reported tea cup sized hail between Altura and Lewiston that shattered a trailer house window and damaged cars. |
| July 2023 | Hail | Altura | $250,000 | Public reported hen egg to tea cup sized hail near Altura resulted in damage to houses and cars. |
| June 2008 | Flash Flood | Lamoille | $250,000 | Flash flooding led to mudslides and damage to sections of County Road 9 along Cedar Creek. Pleasant Valley Creek also had a flash flood. Water flowed into nearby fields as well. |
| June 1998 | Thunderstorm Wind | Lewiston | $250,000 | no account filed |
| May 1982 | Tornado (F2) | not stated | $250,000 | no account filed |
| June 1980 | Tornado (F2) | not stated | $250,000 | no account filed |
| September 2019 | Tornado (EF1) | Winona | $175,000 | A short-lived tornado moved through Woodlawn Cemetery in Winona. The tornado caused extensive damage to trees and gravestones. The roof of a shed was also damaged. |
| July 2023 | Hail | Rollingstone | $150,000 | Public reported tennis ball hail caused holes in siding of a house near Minnesota City. |
| July 2023 | Hail | Altura | $150,000 | Public reported hen egg to tea cup sized hail near Altura. News reported damage to corn crops, house roofs, and cars. |
| May 2022 | Flash Flood | Winona Muni Arpt | $150,000 | Runoff from heavy rains caused mud slides and washouts to occur in the area around Homer with the debris covering several roads. Some cars were submerged in the flood waters. A state of emergency was declared and the Governor of Minnesota authorized emergency assistance to help with the recovery. |
| August 1998 | Flash Flood | Stockton | $150,000 | no account filed |
| May 2024 | Tornado (EF1) | Utica | $120,000 | A fast moving and long track tornado began in St. Charles and produced EF-0 to EF-1 damage to farmsteads and trees in central Winona County. It then moved into Rollingstone, Minnesota were it damaged a few structures and caused widespread tree damage. The tornado continued northeast and crossed the Mississippi River into Buffalo County, Wisconsin where it dissipated. |
| June 2017 | Flash Flood | Stockton | $108,000 | Runoff from heavy rain pushed Garvin Creek out of its banks around Stockton. Debris caught in the flood waters clogged culverts where the creek passes under County Road 23 causing enough dirt to be eroded that a portion of the road collapsed. |
| December 2021 | Tornado (EF1) | Homer | $100,000 | An EF1 tornado formed on a ridge top southwest of Homer, moved northeast across Homer before moving out over the Mississippi River and into Trempealeau County, Wisconsin. The main damage occurred on the ridge top to trees and outbuildings. By the time the tornado reached Homer, it was weakening and damage was mainly limited to trees. |
| December 2021 | Tornado (EF0) | Wyattville | $95,000 | This short-lived EF0 tornado moved over rural areas southeast of Lewiston. Farm outbuildings, a garage and trees were damaged by the tornado. |
| June 2010 | Thunderstorm Wind | Goodview | $95,000 | Thunderstorm winds damaged at least a dozen mobile homes in the Hidden Valley mobile home park. One home was destroyed when a large tree was uprooted and fell on the home. No injuries occurred as the family decided to stay the night with friends. In addition, the roof of a cattle slaughtering plant was damaged in the Bethany area. |
| July 2024 | Flood | Winona | $85,000 | Significant rainfall throughout June pushed the Mississippi River at Winona into flood stage in June and continued into July. The river stage crested during the afternoon on July 2nd in moderate flood stage at 16.14 ft. |
| July 2024 | Hail | Goodview | $85,000 | The public reported 2 inch diameter hail in Goodview. |
| July 2024 | Hail | Rollingstone | $78,000 | Local officials reported 2 inch diameter hail near Rollingstone. |
| August 1998 | Thunderstorm Wind | Winona | $75,000 | no account filed |
| June 2010 | Thunderstorm Wind | St Charles | $65,000 | The Winona County emergency manager reported railroad crossing guard rails and trees blown down. |
| August 2020 | Hail | Ridgeway | $60,000 | Two inch diameter hail was reported near Ridgeway. |
| August 2007 | Flood | Elba | $60,000 | The Middle Fork of the Whitewater River at Whitewater State Park reached a record crest of 19.24 feet. Flood stage is 13.5 feet. The rapid rise of flood waters forced the evacuation of campers throughout the park. |
| July 2023 | Hail | Altura | $55,000 | Public reported hen egg to tea cup sized hail near Altura that broke through a roof of a greenhouse. |
| August 1998 | Thunderstorm Wind | Winona | $55,000 | no account filed |
| July 2023 | Hail | Wilson | $50,000 | Public reported tennis ball sized hail near Winona. |
| July 2023 | Hail | Witoka | $50,000 | Public reported hen egg sized hail in Wilson. |
| December 2021 | Thunderstorm Wind | Hart | $50,000 | A path of wind damage occurred west of Hart where the roof was removed from a farm outbuilding, a metal pole shed was destroyed and siding removed from a house. |
| December 2021 | Thunderstorm Wind | The Arches | $50,000 | A house southeast of Lewiston sustained significant wind damage. |
| December 2021 | Thunderstorm Wind | The Arches | $50,000 | Two open air farm outbuildings were destroyed east of Lewiston. |
| June 2020 | Hail | Homer | $50,000 | Hail ranging in size from 1.75 to 2 inches in diameter was reported south of Homer. |
| June 2010 | Thunderstorm Wind | St Charles | $50,000 | The Winona County emergency manager reported a large grain bin blown over along with power lines down. |
| June 2008 | Flood | Winona | $50,000 | Street flooding was reported in Winona. |
| July 2008 | Thunderstorm Wind | Utica | $50,000 | Thunderstorm wind gusts produced damage to a farm near Utica. Thunderstorm wind gusts also knocked down several elm trees, a 50 foot steel windmill, and blew a metal roof off of a tractor shed. |
| May 1998 | Thunderstorm Wind | Winona | $50,000 | no account filed |
| July 1997 | Flash Flood | Lewiston | $50,000 | no account filed |
| July 2023 | Hail | The Arches | $40,000 | Public reported tennis ball hail fell between Stockton and Lewiston. |
| May 2013 | Thunderstorm Wind | St Charles | $40,000 | Damage to buildings occurred from about 2 miles north of St. Charles to 4 miles north of St. Charles. Large trees were blown down along with a pole barn and corn cribs. Six foot long sections of tin were ripped off other buildings and some one inch hail also fell. |
| May 1998 | Thunderstorm Wind | Hart | $40,000 | no account filed |
| August 1998 | Thunderstorm Wind | Winona | $40,000 | no account filed |
| August 1997 | Flash Flood | Winona | $40,000 | no account filed |
| August 1997 | Thunderstorm Wind | Goodview | $40,000 | no account filed |
| April 2022 | Thunderstorm Wind | Lewiston | $30,000 | At the high school in Lewiston, metal bleachers were ripped off the main seating area, smaller metal bleachers were blown across the track and part of the track was ripped up. |
| December 2021 | Thunderstorm Wind | Stockton | $30,000 | Farm outbuildings sustained wind damage near Stockton. |