Since the Fukushima nuclear accident, seismic design requirements have increased, necessitating a more refined evaluation of base uplift for weakly anchored nuclear island buildings. The elevated cooling water over 3000 t is a distinguishing feature of third-generation reactor buildings (RBs). To assess potential safety-adverse coupling effects, seismic wave propagation process through viscoelastic soils, discontinuous interfaces, and sloshing water was analysed. To facilitate nonlinear systematic simulation and parametric study, the traditional soil-structure interaction direct methods are improved and programmed on: thickness-independent viscous-spring elements for stable static-dynamic boundary transitions; seismic forces separated from the artificial boundary for flexible mesh planning; elevated water simulated with gravity stacking and hydrodynamic action. A nuclear island region encompassing water-cooled RBs and underlying soil cushion layer was investigated as a typical scenario to reveal rules using the proposed high-precision simulation platform. Non-negligible structural risks and correlations between multiple factors were quantitatively elucidated according to simulation findings. A time-lagged increase in the base overturning moment may occur because of water oscillations. As the water level increases to 85 %, the uplift height increases, adversely affecting the in-structure response spectra. Earthquake-induced intense uplift may lead to an increase in hydrodynamic pressure along the inner wall. The research results support the practical assessment of buildings with water cooling facilities located in soft composite sites with high seismic intensities.