Throughout the 1950s and 1960s, the National Park Service undertook many archeological excavations of effigy and burial mounds within the Monument, however when a mound is excavated, its value as a scientific object of study is greatly reduced or destroyed. It was during this time that some people began to question the wisdom of excavating burial and ceremonial mounds. In 1959, Effigy Mounds NM established a policy prohibiting further destructive investigations of the mounds, stating that in the future only nondestructive testing methods would be permitted. By the 1970s the emphasis at the monument had fully shifted away from archeological field investigations and towards preservation and interpreting the mound builder story.
During the 1980s, another shift of emphasis took place, this time the transition being from a more traditional "scientific" perspective to one that viewed the mounds and associated landscape from a more humanistic perspective. While the "science" of the mounds still mattered, the fact that the monument was interpreting what modern American Indians considered to be a "sacred landscape" began to be recognized. The passage in 1990 of The Native American Graves Protection and Repatriation Act (NAGPRA) promoted this shift, and subsequently opened a new chapter in the history of the monument. This act requires Federal agencies and museums that possess Native American human remains and cultural items to consult with lineal descendants and culturally affiliated Indian tribes. Consultation and dialog that began in the 1990s led to the development of long-absent connections between the monument, its affiliated tribes, and the living descendants of the Native American mound builders.