Born in San Juan, Puerto Rico, Estevan Antonio Fuentes was the son of Estevan and Demetria Cherbonnier Fuertes. He received his education at Salamanca, Spain, and at the Rensselaer Polytechnic Institute of Troy, New York.
From 1861 to 1863, he was assistant engineer in the Department of Public Works, Puerto Rico, and subsequently served as director of public works for the western district of that island. Coming to the United States in 1864, he was successively assistant engineer and engineer to the Croton Aqueduct Board, and prepared a valuable report on the connection of the Croton water supply with the manufactures of New York City.
From 1870 to 1871, he was chief engineer of the American Isthmian Canal expeditions to Tehuantepec and Nicaragua to investigate and report on the practicability of a ship canal connecting the Caribbean and the Pacific.
In 1873, he was appointed founding dean of the Civil Engineering Department of Cornell, and from 1890 to 1902 directed the Cornell's College of Civil Engineering advancing its research and technical programs to its then "state-of-the-art" modern standard.
In 1902, he was also appointed professor of astronomy at Cornell and supervised the construction of the A. C. Barnes Observatory.
The Fuertes Observatory (completed in 1917) on North Campus was subsequently named in his honor and remains in his name to this day.
On the international plane, Fuertes also is known for his visionary design and comprehensive planning of the drainage systems of Santos, Brazil.
He was a member of many scientific societies, American and foreign, and published numerous scientific articles and reports.
On December 11, 1860, he married Mary Stone Perry. They had six children: Felix Juan (b. November 20, 1861 Puerto Rico), James Hillhouse, George Perry (April 15, 1865 Brooklyn, New York - October 6, 1878 Ithaca), Sarah Demetria (b. January 6, 1868 Stamford, Connecticut), Mary Katherine (b. March 16, 1872 Stamford) and Louis Agassiz.