During the evening of Sunday, June 28th, a complex of thunderstorms that developed across Iowa previously, moved slowly northward across southern Minnesota and western Wisconsin before stalling Monday morning. During the onset of the heavier rainfall, a few storms caused wind damage near Tainter Lake and Colfax, but most of the damage was minor with a few large tree limbs and power lines blown down.
Deep moisture convergence along the axis of thunderstorms, training along the periphery of the the numerous boundaries, combined with PWAT values of 1.7 to 1.9 inches which is over the 99th percentile value, caused extreme rainfall rates.
Before the flash flooding event developed, there was an hour or two during Sunday evening that dropped locally one to two inches of rainfall in the areas that received more torrential rainfall in the early morning hours.
There was one main band of excessive rainfall that occurred in west central Wisconsin during the early morning. This area was from Prescott, northeast toward River Falls and Baldwin. Based on the return period from precipitation amounts in a specific time frame, the values were a 100-200 year event. Flash flood guidance values were 1.5 to 2 times above normal.
As the runoff continued through the morning, the flash flood event become more areal flooding as the flood waters receded into creeks, streams, and eventually the mainstem rivers. Other areas that experienced flooding but not as significant include the New Richland Golf Course. The St. Croix County Sheriff Office documented the flood damage the next day from their drone. From the video, you could see numerous culverts and roads that were washed away including crop fields (near the creeks and streams) that were inundated nearly 24 hours after the initial rainfall started.
Some of the higher rainfall totals around the area are as follows.
Emerald measured 9.84 inches.
Baldwin measured 8.72 inches.
River Falls measured 6.34 to 7.82 inches around the city.
Roberts measured 7.24 inches.
Menomonie measured 5.08 to 5.64 inches around the city.

Thunderstorm Wind in DUNN, WISCONSIN
From 28-JUN-20 20:55:00 to 28-JUN-20 21:05:00 (CST-6)
Location: WHEELER
Magnitude: 52.00 EG
Property damage: 0.00K
Crop damage: 0.00K
Reported by: Fire Department/Rescue

Several trained spotters and the local fire department around Trainter Lake to Colfax reported a few large tree limbs blown down, along with some power lines.

Flash Flood in PIERCE, WISCONSIN
From 29-JUN-20 04:45:00 to 29-JUN-20 07:45:00 (CST-6)
Location: PRESCOTT
Flood cause: Heavy Rain
Property damage: 0.00K
Crop damage: 0.00K
Reported by: Department of Highways

There were numerous road closures, and culverts overwhelmed by flood waters across portions of Pierce County. Some specific closures included Highway 10 west of Ellsworth, County Road O along the Trimbelle River, and the towns of Martell and El Paso were severely flooded from the Rush River.  In addition, some crops were washed out around Spring Valley.

Flash Flood in DUNN, WISCONSIN
From 29-JUN-20 05:00:00 to 29-JUN-20 08:00:00 (CST-6)
Location: IRVINGTON
Flood cause: Heavy Rain
Property damage: 0.00K
Crop damage: 0.00K
Reported by: Law Enforcement

There were several roads that were closed across Dunn County due to the flooding. There was some mudslides noted between Lake Tainter and Wheeler. County Road W, north of Colfax, had one foot of flowing water over it during the height of the storm.

Flash Flood in ST. CROIX, WISCONSIN
From 29-JUN-20 01:30:00 to 29-JUN-20 04:30:00 (CST-6)
Location: DEER PARK
Flood cause: Heavy Rain
Property damage: 8.00M
Crop damage: 0.00K
Reported by: Emergency Manager

Parts of St. Croix County received over 8 to 9 inches of rain causing flooding and washed out roads across the county. The worst areas that experienced significant flooding were the Kinnickinnic, Rush and Eau Galle Recreation River areas, and the towns of Hammond, Baldwin, Emerald, Glenwood City, and Cylon.
Some of the specific roads that were closed or washed out during the height of the flooding were: 1000 Block of 190th Street in Baldwin, 2100 110th Avenue in Baldwin, Country Road TK, DD & 240th Street in Baldwin, Highway 12 & 220th Street in Baldwin Township, 2254 130th Avenue in Emerald, 2900 Block of 200th Avenue in Glenwood City, and West Blvd & Highway 65 in Roberts.
Unfortunately,  A man died after he lost control while driving on a water-covered road north of Baldwin near County Road E and Highway 63. At least five other motorists standing on the roofs of their cars were rescued from rushing water in that same location in the Baldwin area.
About $4 Million dollars in damages was due to 40 homes that sustained major damage and one that was destroyed when the foundation caved in. The other $4 Million dollars was due to bridge, highway and road damage.