A very anomalous moist atmosphere was in place for this flash flood event to develop. Precipitable water values (PWATs) were over 2 inches across southern Minnesota which is well over climatological normals. The 2.25 inches of precipitable water tallied from the 7 PM weather balloon launch at Chanhassen was just below record record levels for the day and was above the 95th percentile for this time of year.
There were very subtle outflow boundaries during the afternoon from earlier thunderstorms in southern Minnesota. There was enough surface boundary interaction to develop a few funnel clouds where the thunderstorms formed. There were even two tornado touchdowns near Gaylord and a funnel cloud near Lafayette.
The main event was the flash flood event where storms formed Saturday afternoon between Redwood Falls, and the Twin Cities metro area. There were several waves of thunderstorms Saturday evening that propagated east-southeast across far southern Minnesota. The first area was concentrated between Redwood Falls and Henderson, Minnesota. This areas held together for nearly 4 hours before shifting slightly to the southeast toward the Minnesota River. Between 9 PM and 1 AM LST, the heaviest precipitation axis shifted along the Minnesota River Valley from Granite Falls, southeast to New Ulm, Mankato and then toward Waseca. After 1 AM LST, a much broader area of showers and thunderstorms started to develop across the rest of southern and western Minnesota. However, there still remained several hours of moderate to heavy rainfall in the same areas that received the heavier rainfall Saturday evening.
Based on MRMS-FLASH (Multi-Radar Multi-Sensor) (Flooded Locations and Simulated Hydrographs), excessive rainfall rates, and training over the same locations for a long period of time, the first concentrated area of flash flooding occurred over Sibley County where the recurrence interval was over 200 years for the 3, 6, and 12 hour periods. By midnight, this area of 200 year recurrence interval moved westward into southeastern Renville County. Between midnight and 4 AM LST, this area of 200 year recurrence interval moved east-southeast and oriented from Redwood Falls, southeast along the Minnesota River Valley, east/southeast toward Waseca.
The heaviest rainfall and the hardest hit areas in terms of rainfall totals were over southeast Renville, southern Sibley, Nicollet, southwest Le Sueur, northern Blue Earth, and a part of northwest Waseca Counties.
The highest known total for this storm came from a trained observer near Winthrop in Sibley County where they measured 11.50 inches. Other high totals in that area included 10.70 inches near Lafayette and 9.15 inches in Gibbon.
The state climate office categorized the heavy rainfall event in south central Minnesota  as a mega-rain.  Their criteria for a mega-rain is six inches of rain or more over an area of roughly 1000 square miles.  This was the first mega-rain event in Minnesota since 2016.

Heavy Rain in LE SUEUR, MINNESOTA
From 25-JUL-20 06:00:00 to 26-JUL-20 06:00:00 (CST-6)
Location: WATERVILLE
Property damage: 0.00K
Crop damage: 0.00K
Reported by: CoCoRaHS

A measured rainfall report over the last 24-hours at Waterville was 7.33 inches.

Tornado in SIBLEY, MINNESOTA
From 25-JUL-20 17:31:00 to 25-JUL-20 17:38:00 (CST-6)
Location: GAYLORD
Tornado F-scale: EF1
Property damage: 0.00K
Crop damage: 0.00K
Reported by: Storm Chaser

Large branches were lofted when the tornado went through a line of trees, but otherwise the tornado moved across corn and bean fields. The tornado was captured on video by a storm chaser and a local resident.

Heavy Rain in NICOLLET, MINNESOTA
From 25-JUL-20 06:30:00 to 26-JUL-20 06:30:00 (CST-6)
Location: ST PETER
Property damage: 0.00K
Crop damage: 0.00K
Reported by: Broadcast Media

A measured rainfall report over the last 24-hours near St. Peter was 8.50 inches.

Flash Flood in SIBLEY, MINNESOTA
From 25-JUL-20 21:00:00 to 26-JUL-20 03:00:00 (CST-6)
Location: GIBBON
Flood cause: Heavy Rain
Property damage: 0.00K
Crop damage: 0.00K
Reported by: Trained Spotter

There were numerous roads that had water flowing over them, some up to one foot high. This occurred across southern Sibley County, mainly south of Highway 19, south to the Nicollet County line.

Funnel Cloud in SIBLEY, MINNESOTA
From 25-JUL-20 18:29:00 to 25-JUL-20 18:29:00 (CST-6)
Location: WINTHROP
Property damage: 0.00K
Crop damage: 0.00K
Reported by: Trained Spotter

Three different trained spotters saw a funnel cloud just northwest and north of Lafayette.

Thunderstorm Wind in NICOLLET, MINNESOTA
From 25-JUL-20 18:30:00 to 25-JUL-20 18:30:00 (CST-6)
Location: LAFAYETTE
Magnitude: 52.00 EG
Property damage: 0.00K
Crop damage: 0.00K
Reported by: Trained Spotter

Several trees were knocked over and many large branches were broken in Lafayette.

Flash Flood in NICOLLET, MINNESOTA
From 26-JUL-20 01:45:00 to 26-JUL-20 04:45:00 (CST-6)
Location: NORTH MANKATO
Flood cause: Heavy Rain
Property damage: 0.00K
Crop damage: 0.00K
Reported by: Department of Highways

Both ramps to U.S. 169 in North Mankato were closed at Center Street due to flood waters.

Flash Flood in LE SUEUR, MINNESOTA
From 25-JUL-20 22:30:00 to 26-JUL-20 01:30:00 (CST-6)
Location: KASOTA
Flood cause: Heavy Rain
Property damage: 0.00K
Crop damage: 0.00K
Reported by: Department of Highways

Highway 22 was closed due to flood waters south of Kasota, between County road 140 and 298. Based on the amount of rainfall that occurred in a few hours before midnight, more county roads were probably impassable for short periods of time.

Flash Flood in RENVILLE, MINNESOTA
From 25-JUL-20 21:30:00 to 26-JUL-20 00:30:00 (CST-6)
Location: FRANKLIN
Flood cause: Heavy Rain
Property damage: 0.00K
Crop damage: 0.00K
Reported by: Emergency Manager

A couple of roads were closed between County Road 3 and Fairfax, and south along the Minnesota River.

Tornado in SIBLEY, MINNESOTA
From 25-JUL-20 17:37:00 to 25-JUL-20 17:38:00 (CST-6)
Location: GAYLORD
Tornado F-scale: EF0
Property damage: 0.00K
Crop damage: 0.00K
Reported by: Storm Chaser

A brief tornado was filmed by a storm chaser. It hit a few trees and knocked down some large branches.