Submarine groundwater discharge (SGD) is an important component of the local and regional hydrologic cycles, affecting coastal water quality and ecology. However, the influence of subsurface physical barriers widely built in coastal aquifers for seawater intrusion control has not yet been fully understood with respect to the downstream SGD. In this study, we used both laboratory experiments and numerical simulations to quantify the contribution of subsurface physical barriers to the fresh and saline SGD fluxes. Different types of physical barriers, including cutoff wall and subsurface dam, were examined with various structures (e.g., barrier location, height, or penetration depth). The results demonstrated that subsurface physical barriers with different structures resulted in various changes in the location of the freshwater discharge at the aquifer-sea interface, e.g., the discharge location shifted seaward as the cutoff wall moved inland. The water exchange across the aquifer-sea interface was closely related to the structure of subsurface physical barriers. With the increase in the height of subsurface dam or the increase in the depth of cutoff wall, the fresh and saline SGD fluxes revealed a decreasing trend. Generally, the presence of a physical barrier hindered the hydraulic connection between the upstream and downstream aquifers, and the SGD fluxes were reduced compared to those without any barrier. For cutoff walls, the change in wall depths led to decreases in tide-induced saltwater circulation of 25%–33%, density-driven saltwater circulation of 10%–30%, fresh groundwater discharge of 17%–60%, and the total efflux of 18%–36%. Within the effective height range of the subsurface dam, fresh and saline SGD fluxes peaked at the minimum effective height. These findings provide a general framework for the prediction and monitoring of SGD behavior in coastal aquifers where subsurface physical barriers are intended or have been constructed.