| April 1999 | Tornado (F1) | Boonville | $750,000 | A tornado developed 4 miles south of Boonville and moved quickly northeast, damaging a church and downing several trees and power poles 4 miles south of Boonville. Three eighteen-wheelers were overturned. |
| August 2005 | Tornado (F0) | Boonville | $50,000 | F0 gustnado along the leading edge of a line of thunderstorms produced damage to several homes in southwest Boonville. Also roofs torn off trailers, and numerous trees downed. |
| April 1999 | Thunderstorm Wind | Boonville | $50,000 | Thunderstorm winds blew the roof off of a church. |
| June 1994 | Thunderstorm Wind | Boonville | $50,000 | Strong wind tore one-fourth of the roof off a school building. |
| August 1993 | Thunderstorm Wind | Boonville | $50,000 | Strong winds broke large tree limbs and blew down power lines. |
| June 2000 | Thunderstorm Wind | Boonville | $30,000 | Thunderstorm winds gusted to near hurricane strength in Boonville, downing power lines and trees. A vehicle was damaged when a large tree fell on it, and several residents reported damage to their roofs. |
| June 2009 | Hail | Boonville | $10,000 | no account filed |
| August 2011 | Thunderstorm Wind | Boonville | $5,000 | A barn roof was blown off. Large tree branches were down, and power outages were reported. Thunderstorm wind gusts were estimated up to 70 mph. |
| May 2000 | Lightning | Boonville | $5,000 | A house in Boonville was damaged by a lightning strike. |
| March 1993 | Thunderstorm Wind | Boonville | $5,000 | Three billboards were blown down and destroyed at the junction of Interstate 70 and Highway 87. |
| March 1993 | Hail | Boonville | $5,000 | Golfball-size hail was reported by a weather spotter. |
| October 2009 | Thunderstorm Wind | Boonville | $2,000 | A shed was blown onto a truck, and windows were blown out of a house, on Prairie Lick Road. |
| July 2002 | Thunderstorm Wind | Boonville | $2,000 | Minor roof damage reported. |
| October 2007 | Thunderstorm Wind | Boonville | $1,000 | Window blown out of a downtown Boonville building. |
| May 2002 | Thunderstorm Wind | Boonville | $1,000 | Power lines reported down. |
| May 2025 | Thunderstorm Wind | Boonville | - | Downed wires and power outages on the southeast side of Boonville. |
| June 2025 | Thunderstorm Wind | Boonville | - | Downed tree and wires near Sycamore Street in Boonville. |
| June 2024 | Hail | Boonville | - | Quarter size hail was reported south of Boonville. |
| June 2022 | Thunderstorm Wind | Boonville | - | Powerlines were reported down in front of KWRT radio station in Boonville. There were also several trees down across the area. |
| June 2021 | Thunderstorm Wind | Boonville | - | Multiple trees down in and around Boonville. |
| June 2021 | Flash Flood | Boonville | - | Several roads were flooding with running water in Boonville. |
| August 2020 | Thunderstorm Wind | Boonville | - | A maple tree was downed in Boonville. Numerous other tress were damaged or broken. |
| May 2018 | Thunderstorm Wind | Boonville | - | Power lines and a tree came down in Booneville. |
| May 2017 | Thunderstorm Wind | Boonville | - | Emergency Manager reported power lines down near Boonville. |
| March 2016 | Thunderstorm Wind | Boonville | - | Several large trees were blown down in the city of Booneville, Missouri and power outages were reported. |
| September 2014 | Flash Flood | Boonville | - | Highway U and Doyle Road were closed due to high water. Highway 87, 500 feet from Interstate 70 overpass was closed due to high water and several reports of accidents due to hydroplaning. |
| May 2013 | Flash Flood | Boonville | - | One foot of water was reported over U Highway and Doyle Road. |
| June 2009 | Thunderstorm Wind | Boonville | - | Numerous trees were reported blown down. |
| April 2008 | Flood | Boonville | - | The Petite Saline Creek near Boonville crested at 21.68 feet, or 5.68 feet above flood stage. |
| June 2007 | Flood | Boonville | - | The Petite Saline Creek near Boonville crested at 16.85 feet, or 0.85 feet above flood stage. |
| February 2007 | Flood | Boonville | - | The Petite Saline Creek near Boonville crested at 18.25 feet, or 2.25 feet above flood stage. |
| February 2007 | Flood | Boonville | - | Snow and ice melt caused the Petite Saline Creek near Boonville to crest at 17.30 feet, or 1.30 feet above flood stage. |
| April 2006 | Flood | Boonville | - | The Petite Saline Creek near Boonville crested at 16.00 feet, or right at flood stage. |
| July 2006 | Thunderstorm Wind | Boonville | - | Large tree limbs down. |
| May 2004 | Thunderstorm Wind | Boonville | - | Large trees blown down in Boonville. |
| May 2004 | Flash Flood | Boonville | - | County roads under water. |
| June 2004 | Thunderstorm Wind | Boonville | - | Trees reported down on Highway 40. |
| August 2004 | Flash Flood | Boonville | - | Heavy rains caused flooding on several roads. |
| August 2004 | Flash Flood | Boonville | - | Heavy rains caused flooding on several roads. |
| May 2002 | Flash Flood | Boonville | - | Doyle road and U highway closed due to high water. |
| May 2002 | Flash Flood | Boonville | - | U highway near Boonville closed due to high water over the road. |
| August 2001 | Thunderstorm Wind | Boonville | - | Tree blocking highway 90. |
| August 2000 | Thunderstorm Wind | Boonville | - | Boonville police reported 60 mph wind gusts. |
| August 2000 | Hail | Boonville | - | Dime size hail was reported at mile marker 106 on Interstate 70. |
| June 1998 | Thunderstorm Wind | Boonville | - | A spotter reported trees down in Boonville as a result of a 59 MPH gust during a thunderstorm. The damaging thunderstorm winds also blew a 10 inch diameter tree on top of a house in Boonville. |
| June 1998 | Hail | Boonville | - | The Cooper County Sheriff's Office reported dime-size hail during a severe thunderstorm at Boonville. |
| June 1998 | Hail | Boonville | - | Nickel-size hail was reported during a severe thunderstorm in Boonville by the Cooper County Sheriff's Office. |
| March 1998 | Thunderstorm Wind | Boonville | - | The Cooper County Sheriff's office reported a wind gust to 64 MPH in Boonville. On the west side of Boonville, a tree 14 inches in diameter was blown down resulting in a blocked roadway. |
| February 1998 | Heavy Rain | Boonville | - | One to three inches of rain fell over Cooper County on the evening of the 20th and early morning hours of the 21st. This resulted in flooding of roadways. Route U, about 2 miles south of I-70 was completely closed due to high water. |
| July 1997 | Hail | Boonville | - | A severe weather spotter reported half dollar-size hail in Boonville at the intersection of Interstate 70 and Route 87. |
| April 1997 | Thunderstorm Wind | Boonville | - | Severe thunderstorm winds gusted to 70 MPH and knocked down 4 large trees in Boonville near the intersection of 87 Highway and Interstate 70. |
| February 2017 | Hail | Boonville | - | no account filed |
| April 2014 | Hail | Boonville | - | no account filed |
| March 2012 | Hail | Boonville | - | no account filed |
| September 2012 | Hail | Boonville | - | no account filed |
| May 2011 | Hail | Boonville | - | no account filed |
| May 2011 | Hail | Boonville | - | no account filed |
| June 2011 | Hail | Boonville | - | no account filed |
| June 2011 | Hail | Boonville | - | no account filed |
| June 2011 | Hail | Boonville | - | no account filed |