| May 2007 | Tornado (EF2) | Crofton | 3 hurt, $1,000,000 | A grain bin was damaged as this tornado initially touched down along with two or three large power line support structures northwest of Crofton. The tornado tracked toward Lewis and Clark Lake taking the roof off of a house and destroying a garage. The tornado also caused other roof damage as it continued tracking toward Lewis and Clark Lake. When it reached the lake it caused significant damage to a recreation area and marina. The tornado also caused 3 minor injuries when it apparently lifted a large SUV off the ground and carried it a hundred feet or so before setting it down with the windows blown in. Numerous campers and boats were flipped or missing at the recreation area, along with vehicle damage. About $1 million in damage was estimated to have occurred at the recreation area. Many trees were also toppled. This tornado and others in Knox county downed 30 to 40 power poles. A Storage building in the area was also severely damaged. This tornado started as one tornado to the southwest was lifting and a weaker one to the northeast was forming. There were several reports by the public of multiple tornadoes in the area, either from the three tornadoes mentioned here, or from multiple vortexes within this tornado. The tornado crossed Lewis and Clark Lake and did f1 damage in South Dakota. |
| June 2000 | Hail | Crofton | $1,500,000 | A hail storm began northwest of Crofton Nebraska and cut a half mile wide swath of damage down to Hartington in Cedar county. Hail, which at times was baseball size, was driven by 50 mph winds causing extensive damage to cars, windows, siding, roofs and crops in the area. Insurance agents stated that between 1 and 2 million dollars in damage was sustained from around Crofton through Hartington. The worst damage was reported at the junction of Highways 81 and 12, 5 miles east of Crofton. Around the junction of Higways 12 and 81 local agronomists estimated that defoliation of corn was in the 85 to 90 percent range with 35 percent of the crop dead. |
| July 1996 | Hail | Crofton | $25,000 | no account filed |
| September 2010 | Flash Flood | Crofton | $10,000 | Rainfall of over 7 inches was reported in less than 24 hours in the Crofton area. The second round of heavy rain to hit the area during the evening of the 22nd produced flash flooding of streets and a park in Crofton. Two sections of the fence around a baseball field were taken out by flood waters. |
| June 2025 | Hail | Crofton | - | Report of hail, mostly dime sized but a few quarter sized hail stones mixed in. |
| June 2023 | Thunderstorm Wind | Crofton | - | Public reported tree damage. |
| July 2022 | Thunderstorm Wind | Crofton | - | Public reported a tree and large limbs down on a golf course. |
| July 2014 | Thunderstorm Wind | Crofton | - | The gust was measured near Weigland Marina at Lewis and Clark State Recreational Area. |
| June 2011 | Thunderstorm Wind | Crofton | - | Thunderstorm wind gusts estimated at close to 70 mph downed a large tree onto Highway 12 near Crofton. |
| June 2010 | Hail | Crofton | - | The hail occurred with thunderstorm winds estimated at 60 mph. |
| June 2010 | Thunderstorm Wind | Crofton | - | A storm spotter estimated thunderstorm winds of 60 mph winds occurred with dime-size hail west of Crofton. |
| September 2010 | Hail | Crofton | - | Hail up to a little over 4 inches in diameter fell in the Crofton area. The hail lasted at least 15 minutes but was mostly smaller than golf ball-size. |
| September 2010 | Heavy Rain | Crofton | - | A storm total of over 7 inches of rain was reported in the Crofton area. Besides causing flash flooding of a local creek in the area, most basements in the area were flooded by the heavy rain. |
| July 2009 | Heavy Rain | Crofton | - | Rainfall of 1 to 2 inches fell for the second morning in a row in the Crofton area. Due to saturated ground, the rainfall this morning caused some minor flooding around culverts in and around the Crofton area causing ponding of water in a park and softball complex in town. |
| May 2008 | Hail | Crofton | - | The storm also produced 50 mph winds. |
| May 2008 | Hail | Crofton | - | The ground was covered with hail, some up to quarter size. |
| May 2007 | Tornado (EF0) | Crofton | - | This weak tornado apparently touched down just as one tornado to the southwest was lifting and another stronger one, also to the southwest, was just forming along with this one. The 3 tornadoes were caught on video by the public. This tornado did some tree damage and flipped one camper before lifting over Lewis and Clark Lake. |
| May 2007 | Hail | Crofton | - | Reported in the Crofton area by the cooperative observer. |
| June 2006 | Hail | Crofton | - | The hail caused some crop damage in the area. |
| June 2006 | Thunderstorm Wind | Crofton | - | Thunderstorm winds knocked down many large branches and several trees in the Crofton area. |
| June 2006 | Thunderstorm Wind | Crofton | - | Thunderstorm winds estimated at over 60 mph downed large tree branches and overturned a camper at a local campground. |
| June 2006 | Thunderstorm Wind | Crofton | - | Thunderstorm wind gusts estimated at 60 mph blew half the roof off of a machine shed. |
| June 2006 | Hail | Crofton | - | One inch to 1.5 inch hail covered the ground. |
| June 2005 | Hail | Crofton | - | The hail lasted 5 minutes. |
| June 2005 | Hail | Crofton | - | Nickel size hail fell for around 15 minutes from north of Crofton into town. |
| June 2005 | Flash Flood | Crofton | - | Rainfall of 1 to 3 inches fell in an hour or two across parts of Knox county. The rainfall caused flash flooding across Highway 121 that ran 4 inches deep. |
| May 2004 | Hail | Crofton | - | Hail up to dime size covered the ground north of Crofton. |
| August 2004 | Hail | Crofton | - | Hail up to 1 inch in diameter was reported from Crofton to 4 miles north of town. |
| June 2003 | Hail | Crofton | - | Heavy rain was also reported with the hail with 2.5 inches falling in 60 minutes. |
| August 2002 | Hail | Crofton | - | Reported near Gavins Point Dam. |
| August 2002 | Hail | Crofton | - | Hail up to golfball size fell for around 15 minutes in the Crofton area. |
| July 2002 | Thunderstorm Wind | Crofton | - | Thunderstorm wind gusts did extensive damage to some rental storage units north of town on highway 121. |
| July 2001 | Thunderstorm Wind | Crofton | - | A Ham radio operator estimated a thunderstorm wind gust of 65 mph which snapped several large trees in town. |
| June 2000 | Hail | Crofton | - | See narrative above. |
| July 1997 | Hail | Crofton | - | Large hail destroyed a corn crop. |
| April 1994 | Thunderstorm Wind | Crofton | - | Power lines were downed and a house was twisted off of its foundation near Crofton. |
| August 2016 | Hail | Crofton | - | no account filed |
| July 2014 | Hail | Crofton | - | no account filed |
| June 2010 | Hail | Crofton | - | no account filed |
| June 2010 | Hail | Crofton | - | no account filed |
| July 2009 | Hail | Crofton | - | no account filed |
| September 2008 | Hail | Crofton | - | no account filed |
| May 2008 | Hail | Crofton | - | no account filed |
| August 2007 | Hail | Crofton | - | no account filed |
| May 2007 | Hail | Crofton | - | no account filed |
| June 2006 | Hail | Crofton | - | no account filed |
| June 2006 | Hail | Crofton | - | no account filed |
| June 2005 | Hail | Crofton | - | no account filed |
| May 2004 | Hail | Crofton | - | no account filed |
| May 2004 | Hail | Crofton | - | no account filed |
| May 2004 | Hail | Crofton | - | no account filed |
| May 2004 | Hail | Crofton | - | no account filed |
| July 2004 | Hail | Crofton | - | no account filed |
| August 2002 | Hail | Crofton | - | no account filed |
| July 2002 | Hail | Crofton | - | no account filed |
| May 2001 | Hail | Crofton | - | no account filed |
| August 2000 | Hail | Crofton | - | no account filed |
| May 1999 | Hail | Crofton | - | no account filed |
| June 1999 | Hail | Crofton | - | no account filed |
| September 1998 | Hail | Crofton | - | no account filed |