Torrential rain and extreme flooding caused by Atlantic hurricanes mobilize a large pool of organic matter (OM) from coastal forested watersheds in the southeastern United States. However, the mobilization of toxic metals such as mercury (Hg) that are associated with this vast pool of OM are rarely measured. This study aims to assess the variations of total Hg (THg) and methylmercury (MeHg) levels and the isotopic compositions of Hg in a blackwater river (Waccamaw River, SC, U.S.A.) during two recent extreme flooding events induced by Hurricane Joaquin (October 2015) and Hurricane Matthew (October 2016). We show that extreme flooding considerably increased filtered THg and MeHg concentrations associated with aromatic dissolved organic matter. During a 2-month sampling window each year (October–November), we estimate that about 27% (2015) and 78% (2016) of the average amount of Hg deposited atmospherically during these 2 months was exported via the river. The isotopic composition of Hg in the river waters was changed only slightly by the substantial inputs of runoff from surrounding landscapes, in which mass-dependent fractionation (as δ202Hg) decreased from −1.47 to −1.67‰ and mass-independent fractionation (as ∆199Hg) decreased from −0.15 to −0.37‰. The slight variations in Hg isotopic composition during such extreme flooding events imply that sources of Hg in the river are nearly unchanged even under the very high wet deposition of Hg derived from the intensive rainfall. The majority of Hg exported by the river (74–85%) is estimated to have been derived from dry deposition to the watersheds. An increase in frequency and intensity of Atlantic hurricanes is expected in the next few decades due to further warming of ocean surface waters. We predict that increased hurricanes will mobilize more dry-deposited Hg and in situ produced MeHg from these coastal watersheds where MeHg can be extensively bioaccumulated and biomagnified in the downstream aquatic food webs.