Under a newly raised design flood elevation (DFE) for resilience design, many existing buildings need significant structural improvements to meet the structural capacity requirements and comply with the current design standards. The proposed structural improvements are often times not only exorbitantly costly but also face constructability challenges due to site restraints. This paper presents the methodology and results of a numerical transient seepage analysis, which could allow architects and structural engineers to design for a refined, more realistic lateral pressure profile for foundation elements and uplift pressure for interior slabs. The paper summarizes a case study performed at a number of public housing sites in Manhattan, in the close vicinity of the East River. SEEP/W (GeoStudio), a 2-dimensional finite element seepage analysis module, was used to simulate time-dependent, groundwater seepage response primarily due to surface water infiltration. The DFEs were based on the 1-percent annual exceedance probability flood, a required freeboard and a projected future sea level rise. The transient simulations adopted a stage hydrograph (i.e., water level versus time), whose shape closely resembles the observed water levels in the New York Harbor during Hurricane Sandy in 2012. Transient groundwater seepage simulations were performed to evaluate the temporal response in the vicinity of the foundation under the design flood hydrograph.