To address localized seepage issues at the base of deep foundation pits constructed in inclined interbedded strata adjacent to rivers, further research is needed to develop rational groundwater and deformation control strategies. This study examines a deep foundation pit project near the Yellow River in Anning District, Lanzhou City. In response to the distinct characteristics of inclined interbeds, a zoned dewatering scheme combining inclined aquitards with normal partition plates was proposed. Numerical simulations comparatively analyzed differences in supporting structure deformation, groundwater seepage within the pit, and surrounding ground settlement under zoned versus non-zoned conditions. Results demonstrate that under zoned dewatering conditions, groundwater level rapidly declines because of the sealing effect of inclined aquitards and partitions, exhibiting a “trapezoidal serrated pattern” along partition plates. Notably, the design base water level maintains long-term stability after pump cessation, effectively resolving seepage problems at the pit base. Regarding comprehensive control effects—including structural deformation, pore pressure within the pit, and surface settlement around the site—the foundation pit performs better under zoned dewatering conditions than under conventional unzoned conditions.