According to the U.S. Census Bureau, the county has a total area of , of which is land and (2.2%) is water. Brasstown Bald, the highest mountain in Georgia, rises in southeast Union County, straddling the Towns County line. The central and northern portion of Union County is located in the Hiwassee River sub-basin of the Middle Tennessee-Hiwassee basin, while the southwestern portion of the county is located in the Ocoee River sub-basin of the same larger watershed. A very small portion of the county's southeastern corner is located in the Upper Chattahoochee River sub-basin of the ACF River Basin (Apalachicola-Chattahoochee-Flint River Basin, also listed as simply the Apalachicola Basin by USGS). This is also where the source of the Chattahoochee is found.