He entered the Navy in 1861; his military career lasted over a decade and included active duty aboard the gunboat Chocorua and the Nyack in the South Pacific, as well as assignments as an instructor and engineer at the Naval Academy.
Cooper's designs included a broad variety of structures, ranging from the Laredo Shops of the Mexican National Railroad to the furnace plant of the Lackawanna Coal and Iron Company at Scranton, Pennsylvania, but his most memorable contributions were in the area of bridge design.
Also during this period, he served as consultant to numerous commissions charged with the development of rapid transit systems in such cities as New York and Boston.
Cooper was roundly criticized in post-accident reports for his poor judgement and lack of teamwork in the run-up to the disaster.
Cooper is also responsible for developing a system of calculations and standards for the safe loading of railway bridges in 1894. Cooper's loading system was based on a standard of E10, meaning a pair of 2-8-0 type steam locomotives, pulling an infinite number of rail cars.