With the outbreak of the Civil War, all Army officers were withdrawn from the Survey and never returned; all Naval officers but two were withdrawn from Survey duty. Consequently, the civilian officers of the Survey were called upon to serve in the field and provide mapping, hydrographic, and engineering expertise for Union forces for the duration of the war.

Civilian Coast Surveyors, the professional ancestors of today's NOAA Corps, served in virtually all theaters of the war including the defenses of Washington, on the Peninsula with McClellan, with the Union blockading forces, with Farragut and Porter on the Mississippi and Red Rivers, with Grant at Chattanooga and in Virginia, and with Sherman in Georgia and the Carolinas. They were often in the front lines or in advance of the front lines conducting their mapping duties. For its part, the Coast Survey officer force produced many of the coastal charts and interior maps used by Union forces throughout the war.

After the Civil War, the Coast Survey resumed its work of making the shores of our Nation safe for commerce. The area of responsibility continued to grow with the acquisition of Alaska in 1867 and the 1871 law requiring the Coast Survey to carry geodetic surveys into the interior of the country. Naval officers returned to hydrographic duty on the Survey and remained until the Spanish-American War when all were withdrawn permanently. With the acquisition of the Philippines and Puerto Rico, the Coast and Geodetic Survey (C&GS) realm of responsibility increased again. Initial surveys in the Philippines were in support of defense needs as Naval vessels and Army transports grounded on uncharted shoals with distressing frequency.