A graduate of the University of Iowa. He later taught of Zoology at the University of Nebraska from 1888 to 1890, and later returned to the University of Iowa as an instructor in botany. In 1895, he became Assistant Professor in botany and curator of the herbarium, and he continued in the latter position until his death. In 1902 he was awarded a Master's degree in science. He served as head of the botany department at University of Iowa from 1914 to 1919.
Shimek traveled extensively in North America studying nature, and also spent time traveling in Czechoslovakia, and Nicaragua. He especially traveled extensively throughout the American midwest and throughout every region of Iowa. Records show that between 1925 and 1928 Shimek had collected more than 10,000 specimens in Iowa, Nebraska, South Dakota, Wisconsin and Illinois. It has been estimated that, over his lifetime, Shimek contributed 200,000 specimens of vascular plants and 5,000 specimens of bryophytes to the collection.
Shimek worked for the independence of Czechoslovakia. He worked with his personal friend, historian Thomas G. Masaryk, who was exiled to the United States. After Czechoslovakian independence, Shimek was invited to the Charles University of Prague to teach Botany as an exchange professor in 1914. Here he was awarded an honorary Ph.D. in recognition of his scientific contributions. He was also awarded a special Czech medal of honor in 1927.
In a series of papers written in 1890, 1896, and 1898, Shimek concluded that wind (rather than water) was responsible for the deposition of loess in eastern and western Iowa. He based this after extensive study of fossils, habitats, and animal/plant life in the area. This discovery proved to be a major contribution to the study of the environment in the region.
Upon his death Shimek's shell collection contained nearly two and a half million specimens, about half of which are loess fossils. This collection was sold to the Smithsonian Institution, according to his wish.