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Abstract The tidal tributaries of the lower Chesapeake Bay experience seasonally recurring harmful algal blooms and the significance of submarine groundwater discharge (SGD) as a nutrient vector is largely unknown. Here, we determined seasonal SGD nutrient loads in two tributaries with contrasting hydrodynamic conditions, river‐fed (York River) vs. tidally dominated (Lafayette River). Radon surveys were performed in each river to quantify SGD at the embayment‐scale during spring and fall 2021. Total SGD was determined from a²²²Rn mass balance and Monte Carlo simulations. Submarine groundwater discharge rates differed by a factor of two during spring (Lafayette = 11 ± 17 cm d⁻¹; York = 6 ± 10 cm d⁻¹) and a factor of six during fall (Lafayette = 19 ± 27 cm d⁻¹; York = 3 ± 7 cm d⁻¹). Groundwater N concentrations and fluxes varied seasonally in the York (4–7 mmol N m⁻²d⁻¹). In the Lafayette River, seasonal N fluxes (22–37 mmol N m⁻²d⁻¹) were driven by seasonal water exchange rates, likely due to recurrent saltwater intrusion. Submarine groundwater discharge–derived nutrient fluxes were orders of magnitude greater than riverine inputs and runoff in each system. Additionally, sediment N removal by denitrification and anaerobic ammonium oxidation would only remove ~ 1–11% of dissolved inorganic nitrogen supplied through SGD. The continued recurrence of harmful algal blooms in the Bay's tidal tributaries may be indicative of an under‐accounting of submarine groundwater‐borne nutrient sources. This study highlights the importance of including SGD in water quality models used to advise restoration efforts in the Chesapeake Bay region and beyond.