Rainfall ranging from 1.5 to 2.5 inches fell on the steep slopes of the hills and mountains that make up Clay, Nicholas, Webster and Greenbrier counties on June 21, 2016, saturating the ground and setting the stage for what the National Weather Service would describe as a "thousand year" flood two days later.

During the predawn hours of June 23, a pre-frontal trough—an elongated area of relatively low pressure preceding a cold front—began siphoning heat and moisture from the southwest, as it moved from the northwest into the Ohio Valley. The effect caused a series of thunderstorms to take shape and become embedded in rain clouds as they were compressed into a narrow band between the cooler air to the northeast, and the hot, moist, highly energized air surging in from the southwest.

The rain clouds and embedded thunderstorms formed into a line as they swept eastward into West Virginia, in a phenomenon known as "training." The thunderstorms, lined up like cars on a train, dumped heavy rains repeatedly on many areas along the storm corridor before passing into Virginia.

From 6 a.m. on June 23 to 6 a.m. the following day, 8.29 inches of rain fell on White Sulphur Springs, more than doubling the town's previous record one-day rainfall of four inches set on March 19, 1890. Nearby Lewisburg received eight inches of rain during the same period, almost twice its previous rainy day record of 4.06 inches, recorded in 1954. According to National Oceanic and Atmospheric Administration precipitation frequency estimates, such rainfall totals for those places are expected to recur only once in 1,000 years.

As the storm continued into the night, flash flooding in small creeks gave way to the flooding of larger streams. The Meadow River overflowed its banks at Rupert and Rainelle, the Cherry River swept through downtown Richwood, the Elk River inundated the towns of Clendenin and Clay, and Howard Creek raged through White Sulphur Springs and its world-famous Greenbrier resort, forcing the cancellation of the Greenbrier Classic golf tournament, a stop on the PGA tour.

A total of 23 people died in the flood, most of them in Greenbrier County and in the Clendenin area of Kanawha County. More than 1,500 homes and businesses were destroyed, and another 2,500 significantly damaged, while losses to highways and bridges totaled about $53 million.

The 2016 flood was among the deadliest floods in West Virginia history. It is surpassed only by the 1972 Buffalo Creek Disaster in Logan County, where a coal slurry settling pond dam collapsed, sending 132 million gallons of water down a narrow, heavily populated valley, killing 125; the 1916 Cabin Creek flood; the 1985 "Election Day" floods in the state's Potomac, Cheat and Greenbrier River watersheds; and four other floods.

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