Populations of state protected Augusta Shoals spider lily (Hymenocallis coronaria) are declining throughout its southeastern range in Alabama, Georgia, and South Carolina. Artificial flow rates and deer herbivory appear to be the major detriments to the three remaining populations of this species in the Augusta Shoals of the Savannah River, Georgia, where it was first discovered in 1773 by William Bartram. High and fluctuating flow rates in the Savannah River during the May–October portion of the growing season adversely affect flowering and seedling establishment compared to a tributary population in Stevens Creek east of Plum Branch, South Carolina. Water quality parameters and non-deer herbivory were similar in both populations as were asexual ramet formation and general clump size. Seed production and seedling establishment were examined in H. coronaria to determine how these were affected by flow rates. Cooperation between state and federal agencies regulating stream flow rates and deer herbivory are needed to prevent further declines in the Savannah River populations.