For histories of science, environment, and agriculture, SDSU has their Agricultural Experiment Bulletins from 1887 and Research Station reports from 1961 posted online, as well as other department reports and publications. The website is called Open PRAIRIE, link to earliest Bulletins here.
There are a ton of archival resources outside the state that give us insight into South Dakota history. The New York Public Library has an amazing archive and has made many of their collections available digitally. See the 104 results that I found searching for “South Dakota” at this link here.
Historic maps can be critical research tools, but also super fun. The David Rumsey Historical Map Collection is infamous and the 158 results for South Dakota include published atlases as well as exploration maps, territorial maps, railroad maps, soil maps, and tourist maps–link here. Then, the US Geological Survey recently made historical topographic maps available in a new user-friendly platform, link here.