Nevius was born on a farm halfway between the villages of Lodi and Ovid in the "Lake country" of western New York state. It was an idyllic country location surrounded by fields and meadows with a nearby spring of pure water, and Lake Seneca, "gleaming through the trees", only 2 miles distant; he was the son of Benjamin Nevius, of Dutch descent, and his wife Mary Denton. He was educated at the college in Ovid, then at Union College in Schenectady, then, from 1850, at Princeton as a prospective minister in the Presbyterian Church.