Atwater grew up in the New England area. He opted not to fight in the American Civil War and instead to pursue an undergraduate degree at Wesleyan University in Connecticut. In 1868, Atwater's interest in civil engineering and agricultural chemistry led him to enroll in Yale University's Sheffield Scientific School, where he analyzed agricultural fertilizers for specific mineral content. Atwater received his doctorate in 1869 in agricultural chemistry, his thesis being entitled "The Proximate Composition of Several Types of American Maize." Afterwards, he spent two years in Leipzig and Berlin, where he visited agricultural experiment stations. Atwater also spent time traveling throughout Scotland, Rome, and Naples, where he reported his findings in local newspapers distributed where he lived back in the United States. Atwater later returned to the United States to teach at East Tennessee University and later Wesleyan as its first Professor of Chemistry.
Atwater is best known for his studies of human nutrition. He studied respiration and metabolism in animals and in humans. He invented and utilized a machine called the respiration calorimeter. With annual costs exceeding ten thousand dollars, this piece of equipment was considered a dream project for the nineteenth century. The calorimeter aided studies in food analysis, dietary evolution, work energy consumption, and digestible foods. It measured the human metabolism balance by analyzing the heat produced and metabolic rate by a person performing certain physical activities. With this machine, the dynamics of metabolism could be quantified and the balance between food intake and energy output could be measured.
The results from Atwater’s calorimetry study influenced many areas of American life. Most importantly, the calorimeter was a great influence to the growing awareness of the food calorie as a unit of measure both in terms of consumption and metabolism. Atwater reported on the weight of the calorie as a means of which to measure the efficiency of a diet. He stated that different types of food produced different amounts of energy. He stressed the importance of a cheap and efficient diet that included more proteins, beans, and vegetables in place of carbohydrates. Atwater also studied the effect of alcohol on the body. His findings showed that humans generated heat from alcohol much like it would generate heat from a carbohydrate. At a time where the Scientific Temperance Federation and the WCTU doubted the nutritional value of alcohol, Atwater proved that alcohol could be oxidized in the body and used as fuel for the human motor. Information gained from Atwater’s experiments was used by the liquor trade in the promotion of alcohol.