With climate change intensifying risks of extreme precipitation and riverine flooding, reassessing building resilience under multi-hazard scenarios, particularly those involving earthquakes, has become increasingly important. This study proposes an integrated framework for three-dimensional (3D) nonlinear time history analysis (NLTHA) to evaluate structural performance under sequential earthquake and flood events. By coupling advanced Computational Fluid Dynamics (CFD) simulations with earthquake engineering methods, the framework captures the time-dependent interaction of seismic and hydrodynamic forces. This overcomes limitations of previous research that relied on oversimplified flood-earthquake interaction models. The analysis focuses on steel special moment-resisting frame (SMRF) buildings in Los Angeles, California. Thirteen seismic hazard levels and four flood inundation depths are analysed, producing detailed engineering demand parameters (EDPs) for both earthquake-only and combined hazard scenarios. Structural vulnerability is evaluated through ductility and plastic hinge rotation in columns and beams. Results show flooding significantly amplifies EDPs, especially in lower stories and front-facing elements, emphasising the need to revise design and assessment strategies for buildings in flood-prone areas. Furthermore, vortex shedding and asymmetric water flow patterns around corners and side columns increase localised hydrodynamic pressures. This integrated approach provides engineers with a comprehensive framework for analysing structures to withstand future climate-driven multi-hazard events.