| June 1999 | Thunderstorm Wind | Wahpeton | 1 hurt, $75,000 | A 5 year-old boy was injured when parts of a neighbors roof came through a window in his house. He received 10 to 12 stitches on his neck and head from glass cuts. Nearby a garage was blown off its foundation and a boat was lifted into some trees. Another neighbor had a shed destroyed and a fish house, boat, and grain bins were damaged. |
| April 2023 | Flood | Wahpeton | $194,000 | Wahpeton - First crest of 12.29 ft occurred on 4/15, with a secondary crest of 12.51 ft occurring on 4/19.|NOTE: Damages dollar amount is for the entire county. Not separated by specific river basin or damage type. |
| August 2008 | Flash Flood | Wahpeton | $150,000 | Water was reported to be 2 to 3 feet deep in the streets of Wahpeton with water up on front lawns. 2.75 inches of rain fell in two hours. No travel was advised by city officials. |
| June 1999 | Thunderstorm Wind | Wahpeton | $100,000 | A business on Highway 13 reported substantial damage to its machinery and buildings as the high winds came through. A semi truck also was blown over close by. |
| May 1998 | Flood | Wahpeton | $50,000 | no account filed |
| July 2016 | Flash Flood | Wahpeton | $20,000 | Knee deep water was reported over Sixth Street South, along with basement flooding and power outages. |
| July 2008 | Tornado (EF0) | Wahpeton | $10,000 | A brief touchdown occurred in southern Wahpeton. A large tree was snapped and fell on a house. Other minor shingle and tree branch damage occurred nearby. Peak winds were estimated at 80 mph. |
| July 2002 | Lightning | Wahpeton | $10,000 | 35 to 40 homes were evacuated after lightning ruptured a gas line. The residents were allowed to return two hours later. |
| June 2014 | Flash Flood | Wahpeton | $5,000 | Law enforcement reported that 2.50 inches of rain had fallen causing quite a bit of street flooding. |
| July 2002 | Lightning | Wahpeton | $5,000 | Lightning struck a duplex and damaged a stove an other electrical appliances. No fire was reported. |
| May 1996 | Thunderstorm Wind | Wahpeton | $2,000 | no account filed |
| July 2000 | Thunderstorm Wind | Wahpeton | $500 | Large tree branches were blown down. |
| June 2025 | Thunderstorm Wind | Wahpeton | - | Tree damage in Wahpeton. |
| June 2021 | Thunderstorm Wind | Wahpeton | - | Large trees were snapped or uprooted. Timing based on radar analysis. |
| July 2020 | Thunderstorm Wind | Wahpeton | - | Trees were blown down around town. |
| June 2020 | Thunderstorm Wind | Wahpeton | - | A large tree limb was blown down on a house and fence. |
| July 2019 | Funnel Cloud | Wahpeton | - | The funnel cloud was about a mile west of the Wahpeton city limits. |
| July 2019 | Funnel Cloud | Wahpeton | - | One funnel was observed west-southwest of Wahpeton and a second northwest of Wahpeton. |
| July 2019 | Thunderstorm Wind | Wahpeton | - | A few large tree branches were blown down. |
| July 2017 | Hail | Wahpeton | - | Lots of nickel to quarter sized hail was reported. |
| August 2016 | Thunderstorm Wind | Wahpeton | - | Large tree branches were blown down. |
| July 2016 | Hail | Wahpeton | - | Very heavy rain was also reported. |
| August 2013 | Thunderstorm Wind | Wahpeton | - | Wind driven hail produced widespread tree damage across northern and eastern neighborhoods in Wahpeton. Numerous large trees or tree limbs were snapped off near ground level while neighborhoods were littered with smaller branches, leaf debris, and hail. Peak winds were estimated at 75 mph with the strong winds lasting for several minutes. |
| July 2011 | Thunderstorm Wind | Wahpeton | - | Numerous large tree branches and limbs were broken down by strong winds. Sporadic power outages were also observed. |
| July 2011 | Thunderstorm Wind | Wahpeton | - | A tree was blown down onto a road. |
| July 2010 | Hail | Wahpeton | - | The hail ranged in size from 0.88 to 1.25 inches. |
| July 2009 | Heavy Rain | Wahpeton | - | Approximately 3.25 inches of rain fell between noon and 4 pm CST. |
| July 2009 | Funnel Cloud | Wahpeton | - | A series of weak and short lived funnel clouds formed between Wyndmere and Wahpeton. |
| June 2009 | Hail | Wahpeton | - | Quarter sized hail and wind gusts to 50 mph were reported at the North Dakota State School of Science. |
| July 2008 | Funnel Cloud | Wahpeton | - | A persistent wall cloud with funnel was viewed. |
| September 2008 | Flash Flood | Wahpeton | - | Three to five inches of rain fell in 4 hours, which resulted in localized flooding of farm fields and farm access roads. Some street flooding also occurred. |
| June 2006 | Thunderstorm Wind | Wahpeton | - | Tree branches were snapped off across the north side of Wahpeton. |
| June 2005 | Thunderstorm Wind | Wahpeton | - | The wind gust was measured by a Davis weather sensor at the ND DOT weigh station. |
| June 2005 | Flash Flood | Wahpeton | - | 2.44 inches of rain fell in one hour, causing major street flooding. Conditions were the worst again along fifth street south, where cars were stalled in the high water. |
| June 2005 | Flash Flood | Wahpeton | - | About 2.5 inches of rain fell in an hour, flooding several city streets. Some basement flooding and sewer backup was reported. A car and a minivan were both flooded by high water on one street, which didn't drain for nearly 4 hours. Fifth street south in Wahpeton was hit the hardest. |
| June 2005 | Hail | Wahpeton | - | Hail covered the ground near the Red River. |
| June 2005 | Thunderstorm Wind | Wahpeton | - | A tree was blown down in Wahpeton, destroying a mail box. |
| June 2005 | Thunderstorm Wind | Wahpeton | - | A ND DOT RWIS sensor reported a 60 mph wind gust. |
| August 2005 | Thunderstorm Wind | Wahpeton | - | Strong winds snapped trees and downed power lines. |
| April 2002 | Thunderstorm Wind | Wahpeton | - | A 59 mph wind gust was measured at the Wahpeton State College of Science. |
| August 2002 | Flash Flood | Wahpeton | - | Street and basement flooding was reported after 2 to 6 inches of rain fell in a short amount of time. 30 cars were stalled at a number of intersections from the high water. The county courthouse sustained some water damage as well. |
| September 2002 | Hail | Wahpeton | - | The hail was reported along Interstate 29. |
| April 2001 | Flash Flood | Wahpeton | - | Water was reported over roads. |
| July 2001 | Thunderstorm Wind | Wahpeton | - | Trees were downed by the strong wind. |
| July 2001 | Thunderstorm Wind | Wahpeton | - | Numerous trees were blown down. |
| July 2001 | Thunderstorm Wind | Wahpeton | - | A 59 mph wind gust was measured at the ND State College of Science. |
| July 2000 | Flash Flood | Wahpeton | - | Street flooding occurred in Wahpeton, after nearly 2 inches of rain fell. |
| May 2018 | Thunderstorm Wind | Wahpeton | - | no account filed |
| August 2012 | Hail | Wahpeton | - | no account filed |
| June 2009 | Hail | Wahpeton | - | no account filed |
| July 2008 | Hail | Wahpeton | - | no account filed |
| July 2008 | Hail | Wahpeton | - | no account filed |
| June 2006 | Thunderstorm Wind | Wahpeton | - | no account filed |
| June 2005 | Thunderstorm Wind | Wahpeton | - | no account filed |
| June 2005 | Hail | Wahpeton | - | no account filed |
| June 2005 | Thunderstorm Wind | Wahpeton | - | no account filed |
| June 2005 | Hail | Wahpeton | - | no account filed |
| July 2005 | Hail | Wahpeton | - | no account filed |
| June 2005 | Thunderstorm Wind | Wahpeton | - | no account filed |
| August 2005 | Hail | Wahpeton | - | no account filed |