[2] As a young man, Rotch became interested in the newly developing science of meteorology and determined to make this field his lifetime career.

Rotch chose the site because the elevation of 635 feet (194 m) was the highest point within ten miles (16 km) of the Atlantic Ocean anywhere on the East Coast south of central Maine.

His purpose was to establish an institution free from official control where investigations might be independent of prescribed duties and requirements.

Rotch and Leon Teisserenc de Bort, discoverer of the stratosphere, made extensive upper-air kite measurements from ships in the tropical and sub-tropical North Atlantic.

Rotch became the first director of the observatory and maintained it at his own expense until his death in 1912, when he bequeathed it to Harvard University with an endowment of $50,000.

Under Rotch's leadership, the Blue Hill Meteorological Observatory quickly became famous for its pioneering studies of the upper atmosphere.

Rotch was personally known to the leading meteorologists from Europe because he made it a point to attend all of the meetings of the International Meteorological Committee, and on many occasions was the sole American representative.

Rotch continued to work at the Blue Hill Observatory until his death on April 7, 1912, from a ruptured appendix.