When the U. S. Geological Survey was established in 1879, Pumpelly organized the division of economic geology, and as a special agent of the Tenth Census he planned and directed the investigations on the mining industries, exclusive of the precious metals, and prepared volume xv of the "Census Reports" on "The Mining Industries of the United States" (Washington, 1886). From 1879-80, he conducted at Newport, Rhode Island, an elaborate investigation for the National Board of Health as to the ability of various soils to filter spores from liquids and from air. He became a resident of Newport in 1879, and lived there for 44 years.