Charles E. Bessey's scientific and administrative contributions were diverse and exceptional. He was director and founder of two leading university botany programs. He devised a classification system for flowering plants that has become, with minor revisions, a standard. He directed a tree-planting experiment that eventually led to the formation of the Nebraska National Forest, the first artificial national forest in the world. He helped establish the federal program to fund state agricultural experiment stations. He also used his influence to promote a number of far-sighted causes, including the preservation of wildflowers and legal protection of California's Sequoia trees (Pool, “Professor Charles Edwin Bessey, Master Teacher”).

Bessey was a long time advocate of experimentation as a benefit to agriculture, and when in the early 1880's the United States Department of Agriculture considered setting up research centers, he was consulted. On March 2, 1887 Bessey helped pass the Hatch Act. This act helped establish research centers, called experiment stations, in connection with Morrill Act land-grant colleges. This act also provided a yearly appropriation of $15,000 to each state with which to use for conducting research. Four weeks after this act was passed, the Nebraska legislature moved to take advantage of the offer, and thus, the Nebraska Agricultural Experiment Station was created. Even though $15,000 wasn't a huge sum of money at the time, it was enough to entice the legislature into committing Nebraska to a long term program. This is one of the more prominent things Bessey did for UNL throughout his tenure there. Because of his help in passing the Hatch Act, UNL became nationally known as one of the most respected research colleges in America (Sanders, 66-67).

In 1891 the United States Department of Agriculture's Division of Forestry established a small, experimental plantation of pine trees on the Bruner Brothers' ranch in Hold County, Nebraska. This success led to the creation of two forest reserves on the Dismal and Niobrara rivers by proclamation of President Theodore Roosevelt in April 1902. In 1908 the reserves became the Nebraska National Forest. The Dismal River near Halsey was later renamed for Charles Bessey, and the Niobrara reserve became the McKelvie National Forest in 1971 (Bejot).

Bessey took his research very seriously, and he would have done anything to make sure that his research was accurate. He gave primary place to fundamental research at UNL. He also often wrote of his research in the Daily Nebraskan, usually on a weekly basis. He saw a university as a kind of research center where scientific experiments searched out fundamental principles underlying natural experience. Bessey strongly believed that education was to be oriented to research. Bessey changed the University not into a trade school, but  into an institution of higher learning. Bessey's shadow has since fell on the University for the past century (Knoll, 22).