| Shepherd Branch | rises in N Buncombe County and flows SW into Flat Creek. |
| Shepherd Branch | rises in W Yancey County and flows SE into Bald Creek. |
| Shepherd Creek | rises in N Macon County and flows S into Cowee Creek. |
| Shepherd Creek | rises in E Swain County and flows NW into Kirkland Creek. |
| Shepherd Knob | N Mitchell County on Shepherd Mountain. |
| Shepherd Millpond | on Briery Swamp in NE Pitt County. |
| Shepherd Mountain | W Henderson County on South Fork. |
| Shepherd Mountain | N Mitchell County between Bean Creek and Spring Creek. |
| Shepherd Mountain | W Randolph County between Little Caraway Creek and Uwharrie River. Alt. 1,390. |
| Shepherd Run | rises in S Greene County and flows NE into Contentnea Creek. Named for the Sheppard family, which has lived in the vicinity since the colonial period. |