Moundville was mentioned by E. G. Squier and Edwin Hamilton Davis in their work, Ancient Monuments of the Mississippi Valley (c1848), a survey conducted for the Smithsonian Institution. Later in the century, Nathaniel Thomas Lupton created a fairly accurate map of the site.
Little excavation work was conducted at Moundville by the Bureau of Ethnology's Division of Mound Exploration, partly because the landowner imposed a fee. The first significant archaeological investigations were not conducted until the early 20th century, by Clarence Bloomfield Moore, a lawyer from Philadelphia. He dug extensively at Moundville in 1906, and his detailed records of his work and finds have been of use to modern archaeologists. But looters dug into the mounds over the next two decades and took many artifacts, in addition to destroying stratigraphy of some structures.
In the mid-1920s concerned citizens, including Walter B. Jones (geologist) (after whom the site's museum is named) had begun a concerted effort to save the site. With the help of the Alabama Museum of Natural History, they purchased the land containing the mounds. By 1933 the site had officially become known as Mound State Park, but the park was not developed for visitors until 1938. During this period of the Great Depression, workers of the Civilian Conservation Corps were brought in to stabilize the mounds against erosion. They also constructed roads and buildings to allow public uses at the site. The name of the park was changed to Mound State Monument and was opened to the public in 1939.
During a 1980 break-in at the Erskine Ramsay Archaeological Repository at Moundville, 264 pottery vessels, one fifth of the vessel collection curated by the Alabama Museum of Natural History, were stolen. The highest-quality specimens were taken. Despite an investigation by the Federal Bureau of Investigation, none of the artifacts was seen again until 2018 when three ceremonial bowls were anonymously returned.