[2] Vaughan participated in a number of geological surveys of the West Indies (1901 and 1914), Panama Canal Zone (1911), the Dominican and Haitian Republics (1919 to 1921), the Virgin Islands and eastern Puerto Rico (1919), and the Atlantic and Gulf Coast Plains (1907–1923).

He investigated the corals of Florida and the Bahamas from 1908 to 1915 under the auspices of the Department of Marine Biology of the Carnegie Institution of Washington.

While serving on the Committee on Oceanography for the National Academy of Sciences in the 1930s, Vaughan favored the creation of an east-coast counterpart to the Scripps Institution, and the committee encouraged the Rockefeller Foundation to provide one million dollars to found the Woods Hole Oceanographic Institution.

In 1933 he was given a private audience with Emperor Hirohito and presented with a cloisonné vase, and in 1940 was decorated with the Order of the Rising Sun Third Class.

He kept abreast of research in his fields of interest thanks to assistance from friends and students, who would read scientific literature to him for a few hours each day.