Although the capability of computational fluid dynamics (CFD) in modeling ship hydrodynamics is well explored in many studies, they still have two main limitations. First, those studies ignore the effect of non-uniform shear current which exists in realistic situation. Second, the focus of most studies was laid more on the seakeeping/maneuvering performance and less attention was paid to survivability of ships due to extreme ship response events in waves, which are considered rare events but influential. In this thesis, we explore the capability of CFD in those two areas. In the first part of the thesis, the hydrodynamic performance of KCS in the presence of a non-uniform shear current is investigated for the first time using high-fidelity CFD simulations. Various shear current conditions with different directions were considered and results were compared with the ones with no shear current. The second part of the thesis focuses on study of rare events of ship responses by development of extreme response conditioning techniques to design the wave trail. Two conditioned techniques based on Gaussian and non-Gaussian processes are considered.