Abstract Coastal aquifers are threatened by seawater intrusion (SWI) from sea‐level rise (SLR) and storm surges. Vulnerability is highest in urban areas, where dense populations rely on fresh groundwater and saltwater can damage subsurface infrastructure. The effects of deep building foundations on transient SWI and recovery remain insufficiently understood. Three‐dimensional variable‐density simulations show that, at quasi‐steady state, low‐permeability foundations displace the interface slightly landward by reducing the effective flow cross‐section. Under SLR, foundations slow intrusion once saltwater reaches the foundation zone. Under storm surges, buildings with full‐depth foundations in the low‐permeability aquifer reduce peak whole‐aquifer excess salt mass by 38.8% and prolong its 90% flushing time by 41 years relative to the case without foundations. Aquifer permeability controls foundation‐zone salinization timing and post‐surge recovery rates. By stalling saltwater and impeding flushing, foundations may accelerate their corrosion, even without groundwater pumping. As coastal cities expand, the presence of foundations may exacerbate stresses on urban freshwater resources and infrastructure.