Much of the Lewis & Clark Route east of the Continental Divide is likely to be impacted by serious flooding this spring and summer. The Upper Missouri River Basin has received near-record snowfall this winter and areas to the south of the snow line have received extensive rains, as well. Soils are saturated and flooding has already become devastating in Nebraska and Iowa.
See attached image of 3-month "Percent of Normal" precipitation for U.S.
The northern Great Plains have received anywhere from two to five times normal precipitation, much of that as snow, which is just beginning to melt. The flooding is likely to be as serious at the floods of 2011 - which were called a "once in a century" event. Only 8 years later massive flooding is on the horizon - and could be worse than 2011 if spring rains are excessive. Bear in mind that the region gets nearly half its annual rainfall in May and June.
Here are a couple of links to the current flooding in Nebraska - with bridges and roads washed away.
http://newschannelnebraska.com/local-news/highway-13-bridge-near-hadar-collapses/https://www.nbcnews.com/news/us-news/midwest-flooding-prompts-rescues-evacuations-n984086Although Nebraska Highway 13 is not on the Lewis & Clark, damage to primary roads in the region will take precedence in repairs. Any major damage to secondary roads that are part of the L&C is likely to face significant delays in repair - quite possibly not until next year.
Although flooding will occur later along the Lower Missouri, it is highly unlikely that any part of the Missouri Valley will escape significant flooding. The worst months will be May and June in the Upper Missouri, with flooding extending into July on the Lower Missouri.
In addition to the Lewis & Clark, other ACA routes likely to be impacted are:
Northern Tier - Eastern Montana, North Dakota, Minnesota.
Great Rivers - The Mississippi Valley is likely to have at least moderate flooding, as well.
Katy Trail - The eastern 2/3s is likely to be closed for extended periods.
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Even if roadways are open many park and camping areas are likely to be disproportionately impacted as they are often located on lakes and waterways. In addition, parklands are frequently sacrificed to flooding to focus protection on developed areas.