Abstract We evaluated the influence of groundwater–seawater interaction on mercury dynamics in Maunalua Bay, a coral reef ecosystem located on the south shore of Oʻahu, Hawaiʻi, by combining geochemical data with submarine groundwater discharge (SGD) rates. During a rising tide, unfiltered total mercury (U-HgT) concentrations in seawater increased from ∼6 to 20 pM at Black Point (west Bay) and from ∼2.5 to 8 pM at Niu (central Bay). We attribute this change to an increase in suspended particulate matter at high tide. Approximately 90% of mercury in groundwater at Niu was in the filtered (<0.45 μm) fraction, with a concentration of ∼4 pM. Groundwater discharge during a period of amplified SGD at Niu appeared to contribute to an increase in total mercury concentrations in filtered seawater (F-HgT; 1.2 to 2.4 pM) and in unfiltered seawater (U-HgT; 2.5 to 3.2 pM). The larger magnitude of change in F-HgT relative to U-HgT suggests mercury complexation and/or solubility dynamics in seawater were altered by the addition of groundwater. We used site specific 222Rn derived SGD flux estimates and groundwater F-HgT concentrations to calculate mercury loadings at Black Point (∼3 nmol m−2 d−1) and at Niu (∼1 nmol m−2 d−1). We calculated a weighted average Maunalua Bay groundwater mercury flux of 0.68 ± 0.67 mol yr−1 by combining the proportional flux of F-HgT from three distinct SGD zones, and place these results into a broader context by comparing and contrasting flux estimates from locations around the world. Results from existing SGD studies should be evaluated to develop future sampling strategies that address more targeted questions about mercury biogeochemical cycling at the groundwater–seawater interface.