During Aughey's 13 years of teaching at the University of Nebraska, he published many articles on the importance of quality farming practices, descriptions of Nebraska flora and fauna, the geology of Nebraska, and the soil qualities and sediments of Nebraska. Many of these publications were well respected at the time, and often over practical subjects. However, in later years Aughey was criticized for a lack of "scientific precision" by historian George E. Howard, as well as botanist H. J. Webber.Aughey began the state herbarium with specimens he collected himself and acted as a founder of botany and the natural sciences in Nebraska.

Aughey was a great supporter of the future of the state of Nebraska, and often spoke of possible coal deposits in the Southeastern portion of the state, which never presented themselves. His assurance that this coal would solve "any and all energy shortages for the state" may have been motivated by personal financial interests in the development of coal within the state. In fact, the university administration reprimanded professor Aughey several times on the amount of time and energy he spent investigating coal deposits and resources in Nebraska and Wyoming. His writings on "The Rain Follows The Plow" theory, in which cultivation of land increases precipitation, were flawed, however optimistic. His publications on Nebraska flora, fauna, and sediments were often promoting the settlement of the territory, rather than painting an accurate picture of the land. Some questioned Aughey's scientific accuracy and ethics in his descriptions.

However, Aughey was a popular figure at the university and helped secure its support by the public, who viewed him as their own personal "scientist". After the scandal of Aughey's scientific credulity, his prospecting in coal deposits, and several shady real estate speculations, the public's feelings about Dr. Samuel Aughey began to sour. Aughey offered to resign his position at the university to save face.

This scandal left its mark not only on Aughey, but his children. Aughey's only surving child, Helen, later wrote the chancellor of the University of Nebraska to endow a scholarship in her father's name. However, she requested that the matter of her father's charges and trials be cleared, as they had hounded him even after he left the university.

Aughey went on to work as a geologist in Wyoming and Washington, and died at 84 on February 3, 1912.