| May 1996 | Thunderstorm Wind | Oak Center | $12,000,000 | no account filed |
| September 2010 | Flood | Zumbro Falls | $5,200,000 | Major flooding occurred in the town of Zumbro Falls as the Zumbro River rose to record levels. Of the 95 homes in the town, 60 were affected by flood waters. Businesses in the downtown area also saw damages, while propane tanks were seen floating around. The entire town was evacuated, while power, water and septic systems were down for days. The rainfall as of 5:30 a.m. CST on the 23rd amounted to 6.37 inches. |
| September 2010 | Flood | Hammond | $4,590,000 | Major flooding occurred in the town of Hammond due to record flooding on the Zumbro River. Of the 75 homes in the town, 19 were damaged and 20 were destroyed. Power, water and septic services were down in the town for several days. Businesses in the town also saw extensive damage. |
| September 2010 | Flood | Plainview | $4,500,000 | Flooding occurred along rivers, streams and creeks as well as low-lying areas throughout the county. At least 14 roads were closed across the county due to water over the roads, including U.S. Highway 63, State Highways 68 and 60, and County Roads 3, 8, 21, and 11. At least 10 schools throughout the county canceled classes due to road closures. It was estimated that 300 homes were affected by flood waters throughout the county, 99 of which were in the towns of Zumbro Falls and Hammond. The areas that saw the worst flooding included locations along the Zumbro River, including the cities of Zumbro Falls, Hammond, Millville, and Jarrett. Due to the rising river, the towns of Zumbro Falls, Hammond, and Millville were evacuated, as well as 20 to 30 residents who lived along County Road 11 between Hammond and Millville. In Kellogg, massive erosion occurred along the Zumbro River, which endangered some homes. |
| September 2010 | Flood | Zumbro Falls | $3,500,000 | Locally heavy rains pushed the Zumbro River in Zumbro Falls out of its banks starting on September 23rd. The river gage failed during the flooding and the river is estimated to have returned to within it banks on the 27th. The crest was determined by an USGS survey to have been 35.8 feet, which exceeded the flood stage by almost 18 feet. This crest also established a new flood of record. Numerous homes were heavily damaged or destroyed. |
| August 2007 | Flash Flood | Elgin | $1,200,000 | Flash flooding quickly hit area creeks, even into the Millville, Plainview, and Zumbro Falls area. Several roads were closed as flood waters peaked overnight including damage to some businesses and homes. A few mudslides hit County Roads 2 and 11, among other areas, including a huge boulder that washed on to a road at the start of the flooding. At least 44 families were impacted in Elgin with lower numbers in other communities. |
| August 2010 | Thunderstorm Wind | Lake City | $1,050,000 | Hundreds of trees and at least a half dozen power poles were blown down throughout the city of Lake City. Damage was also reported to several homes as well as to a 100,000 bushel grain bin and a dryer at a local business. The grain bin was destroyed. |
| April 2026 | Hail | Lake City | $820,000 | The public reported 2 inch diameter hail in Lake City. This resulted in damage to structures and vehicles in portions of the city. |
| June 1998 | Thunderstorm Wind | Zumbro Falls | $560,000 | no account filed |
| May 2012 | Thunderstorm Wind | Oak Center | $500,000 | As a severe thunderstorm moved across the northern section of Wabasha County it dropped large hail damaging around 30 percent of the county's alfalfa crop. On farms near Lake City, up to 80 percent of the alfalfa crop was damaged, one cow was killed and irrigation systems were twisted by the wind. |
| August 2007 | Flash Flood | Elgin | $400,000 | County Highways 2 and 25 were closed near the Wabasha/Olmsted county line. |
| September 2019 | Tornado (EF0) | Lake City | $250,000 | An EF0 tornado moved through Lake City. Along the path of the tornado, numerous trees were downed with some landing on houses and mobile homes. The roof of a building was blown off heavily damaging a bank. Some boats that were dry docked at a marina were blown over. |
| August 2007 | Flood | Zumbro Falls | $250,000 | Law enforcement officials reported some roads washed out or still under water. Highways 60 and 63 remained closed. |
| May 1982 | Tornado (F2) | not stated | $250,000 | no account filed |
| August 1964 | Tornado (F2) | not stated | $250,000 | no account filed |
| June 2021 | Hail | Conception | $150,000 | Hail up to 2.5 inches in diameter fell near Conception. |
| August 2016 | Flash Flood | Theilman | $150,000 | Near Theilman, County Road 86 had a washout and debris over the road and a mudslide covered a portion of County Road 4. Flood waters from West Indian Creek rushed through a campground, damaging several campers and took out a snowmobile bridge. |
| October 2013 | Lightning | Hammond | $149,000 | A house south of Zumbro Falls was destroyed by a fire apparently started from a lightning strike. Nobody was home at the time of the fire and two fire departments were on the scene for five hours. |
| May 2022 | Hail | Plainview | $125,000 | Hail ranging in size from golf ball to tennis ball fell north of Plainview. |
| September 2010 | Flash Flood | Kellogg | $125,000 | Mudslides occurred along the Zumbro River along County Road 81, between State Highway 60 and U.S. Highway 61. |
| April 2026 | Hail | Oak Center | $95,000 | A trained spotter reported tennis ball sized hail about 4 miles north-northwest of Oak Center. |
| June 2025 | Tornado (EF1) | Zumbro Falls | $95,000 | This tornado touched down north of Zumbro Falls and ripped the roof off a mobile home residence, also damaging nearby and heavily damaging a barn on 363rd Avenue. It continued for another 1.5 miles northeast across mostly rural areas and causing sporadic tree damage before dissipating. |
| April 2026 | Tornado (EF1) | Elgin | $90,000 | This tornado moved into Wabasha County from Olmsted County and damaged outbuildings and one residence along its path before dissipating near the intersection of County Road 2 and 550th Street. |
| April 2026 | Tornado (EF2) | Elgin | $90,000 | This tornado continued into Wabasha County from Olmsted County where it damaged one residence, some farm outbuildings, power poles, and trees before dissipating near 230th avenue. |
| August 2016 | Flash Flood | Maple Spgs | $90,000 | Several washouts and mudslides occurred on U.S. Highway 61 south of Lake City and along County Roads 4 and 10. |
| June 1998 | Thunderstorm Wind | Plainview | $85,000 | no account filed |
| July 2024 | Hail | Plainview | $82,000 | The public reported golf ball sized hail in the town of Plainview. |
| June 2021 | Hail | Kellogg | $70,000 | Hail up to two inches in diameter fell southwest of Kellogg. |
| July 2008 | Hail | Lake City | $68,000 | Hail of 2.25 inches in diameter was observed. |
| December 2021 | Tornado (EF1) | Plainview | $65,000 | An EF1 tornado developed southeast of Plainview and moved northeast across rural portions of southern Wabasha County. Farm outbuildings and trees were damaged along the path of the tornado. |
| July 2016 | Thunderstorm Wind | Mazeppa | $60,000 | A grain bin and farm outbuildings were damaged north of Mazeppa. |
| May 2012 | Flash Flood | Bellechester | $60,000 | Locally heavy rains across the north half of Wabasha County produced mudslides on U.S. Highway 61, caused water to go over County Road 15 at the intersection with U.S. Highway 63 and flooded basements. |
| June 1999 | Thunderstorm Wind | Elgin | $60,000 | no account filed |
| May 2022 | Hail | Hammond | $55,000 | Up to tennis ball sized hail fell southwest of Hammond. |
| June 1998 | Flash Flood | Zumbro Falls | $55,000 | no account filed |
| June 1998 | Thunderstorm Wind | Zumbro Falls | $55,000 | no account filed |
| March 1998 | Hail | Zumbro Falls | $50,000 | no account filed |
| May 1998 | Thunderstorm Wind | Lake City | $45,000 | no account filed |
| December 2021 | Thunderstorm Wind | Elgin | $40,000 | A barn was destroyed northeast of Elgin. |
| July 2000 | Hail | Lake City | $40,000 | no account filed |
| June 1999 | Thunderstorm Wind | Elgin | $40,000 | no account filed |
| June 1998 | Thunderstorm Wind | Zumbro Falls | $40,000 | no account filed |
| May 1998 | Thunderstorm Wind | Wabasha | $40,000 | no account filed |
| June 2021 | Hail | Conception | $35,000 | Hail up to two inches in diameter fell west of Kellogg. |
| June 1998 | Thunderstorm Wind | Lake City | $35,000 | no account filed |
| July 2024 | Hail | Zumbro Falls | $34,000 | Local fire and rescue reported golf ball sized hail near Zumbro Falls. |
| April 2026 | Hail | Oak Center | $31,000 | The public reported 2 inch diameter hail about 7 miles north of Oak Center. |
| July 1998 | Thunderstorm Wind | Zumbro Falls | $27,000 | no account filed |
| May 2019 | Flood | Reads Lndg | $26,000 | Flooding along the Mississippi River at Wabasha that began in March, temporarily ended in early May. |
| December 2021 | Thunderstorm Wind | Plainview | $25,000 | A large pole shed was extensively damaged in Plainview. |
| December 2021 | Thunderstorm Wind | Plainview | $25,000 | A barn was destroyed southeast of Plainview. |
| June 2012 | Thunderstorm Wind | Theilman | $25,000 | Near Theilman, a two foot diameter tree was snapped in half and a barn was completely destroyed. |
| June 1998 | Thunderstorm Wind | Mazeppa | $24,000 | no account filed |
| July 2016 | Thunderstorm Wind | Oak Center | $20,000 | A barn was blown down and a home damaged southwest of Lake City. |
| July 2024 | Thunderstorm Wind | Elgin | $15,000 | The public reported a tree down on a house and a vehicle southwest of Elgin. |
| September 2018 | Flash Flood | Zumbro Falls | $15,000 | Runoff from heavy rain caused flooding to occur across portions of Wabasha County. Water was over parts of State Highway 60 and some secondary roads had washouts. |
| July 2015 | Tornado (EF0) | Conception | $15,000 | A small, short-lived tornado damaged some corn, removed the tops off of two silos, blew in garage doors and moved tires off a sileage pile. |
| May 2012 | Thunderstorm Wind | Wabasha | $15,000 | A wind gust to 74 mph was measured in the city of Wabasha which blew trees down and caused power outages. |
| August 2007 | Flood | Zumbro Falls | $15,000 | The Zumbro River reached a crest of 21.76 feet, forcing the closure of Highways 60 and 63 for a time. Flood stage is 18.0 feet. |
| August 2000 | Hail | Elgin | $15,000 | no account filed |