Hurricane Fran first made landfall near Cape Fear, North Carolina on September 6th, 1996. While the storm began as a Category 3 hurricane, its strength rapidly weakened upon landfall and it was classified as a tropical storm for most of its time inland. Even in its weakened state, the storm was still responsible for 27 fatalities and $3.2 billion worth of damage. The areas that were hit hardest were the coastlines of the Carolinas and Virginia, but up to 15 inches of rain were also measured along the Appalachian Mountains, with the Blue Ridge Mountains of Virginia and West Virginia taking the brunt of the rainfall.

The rain brought in by Hurricane Fran could not have come at a worse time for the region. The hurricane brought buckets of rain into an area that was already overly saturated from a previous storm only days prior. This meant that Fran, which was already producing much more rain than usual due to ideal environmental events, caused severe flooding as the soil was too saturated to absorb much of the rain. The level of flooding was comparable to other extreme storms that had hit the area previously, such as Hurricane Juan (1985), Agnes (1972), and Dianne (1955). The worst of the flooding occured in the Shenandoah River watershed of Virginia.

Shenandoah National Park had to close its trails and all of Skyline Drive following the storm. While not as many as the Great New England Hurricane, there were still substantial numbers of trees that had been downed during the storm. Skyline Drive had to be slowly reopened as it was inspected for damages to its infrastructure. The park itself had to be slowly reopened as the flooding had caused significant damage to roads and steep retaining walls which all needed to be repaired and inspected. One southbound thru-hiker, Suzanne Hill, stated her relief at being told to vacate the trail following the storm. She stated that due to the debris and damage, "We were hiking 22 miles a day before the storm hit. Now we're down to less than 13 a day. I ripped a hole in my shorts trying to step over, under and around all the trees on the trail." Rangers and volunteers worked hard to clear out the debris, but it took significantly longer due to bad weather and resources being diverted to a missing person in the region.