In the early 1890s, the railroad moved much of its divisional operations to Helper, cutting the Green River population by more than half. This boom-and-bust cycle was to be repeated several times in the twentieth century. An oil boom in 1901 brought a rush to locate claims and some drilling activity but no commercial production. In 1906 a land developer named E.T. Merritt began promoting Green River as a fruit-growing area comparable to the Grand Valley of Colorado. Several hundred acres of peach trees were planted on both sides of the river, but problems with the irrigation system and harsh winter temperatures killed most of the trees before they could come into production. The southeastern Utah uranium boom of the 1950s provided a temporary economic stimulus. More important was the establishment of the Utah Launch Complex of the White Sands Missile Base in 1964, which brought the town's population to a high point of almost 2,000 before the closing of the complex in the 1970s led to yet another economic downturn.

Each of these boom cycles had some lasting impact upon the community. The "Farrer Subdivision" that makes up the southeastern portion of the town was a product of the railroad era. The "upper town" to the north and west was developed during the peach boom, a period that also saw the incorporation of the town in 1906 and the building of a high school in 1910. The Community Presbyterian Church was also established during this period. A Latter-day Saint ward was organized in 1904, disbanded in 1915, and reestablished in 1923. During the uranium boom, Jim Hurst developed an innovative flying service to carry workers and supplies to remote mining locations. The successors to Hurst's operation now carry on an active business flying river running parties. The "missile base" era brought new schools and civic services and saw the Community Church become the Green River Bible Church. Catholic and Baptist worship services were also instituted during this period.