He was born into a Quaker family in Philadelphia, Pennsylvania, son of Edward M. Davis and Maria Mott Davis (a daughter of the women's advocate Lucretia Mott). He graduated from Harvard University in 1869 and received a Master of Engineering in the following year.
He then worked in Córdoba, Argentina for three years, then after working as an assistant to Nathaniel Shaler, he became an instructor in geology at Harvard, in 1879. (Davis never completed his PhD.) He married Ellen B. Warner of Springfield, Massachusetts in the same year.
His most influential scientific contribution was the cycle of erosion, first defined around 1884, which was a model of how rivers create landforms. Though the cycle is considered overly simplistic today, it was a crucial early contribution to geomorphology.
It suggests that (larger) rivers have three main sections: upper course, middle course, and lower course - each of which has distinct landforms and other properties associated with it.
Davis retired from Harvard in 1911. After his first wife died, Davis married Mary M. Wyman of Cambridge, Massachusetts in 1914, and, after her death, he married Lucy L. Tennant of Milton, Massachusetts in 1928, who survived him.
He died in Pasadena, California, shortly before his 84th birthday.