 He opted not to fight in the American Civil War, instead pursuing his undergraduate education, first at the University of Vermont and then moving to Wesleyan University in Connecticut, where he would complete his general education in 1865.For the next three years, Atwater was a teacher at various schools and in 1868, he enrolled in Yale University's Sheffield Scientific School, where he studied agricultural chemistry under William Henry Brewer and Samuel William Johnson.During his time at Yale, Atwater worked part time as Johnson's assistant analyzing fertilizers for specific mineral content; he also performed the first chemical analysis of food or feed in the United States.