This study aims to identify earthquake intensity measures (IMs) that have a reasonable correlation with pore water pressure (PWP). Moreover, the effect of earthquake frequency contents on site response is also investigated. To this end, the centrifuge model test (RPI2) soil profile used in the LEAP-2017 project and twenty input ground motions are employed to conduct effective stress analyses utilizing the one-dimensional (1D) site response analysis (SRA) program. The stress-based simulation model is first validated with centrifuge test results. Afterwards, two sets of analyses are carried out: (1) the analyses with twenty recorded motions to determine the optimal IM for PWP, (2) the analysis with scaled motion to examine the effect of earthquake frequency content. The numerical results show that peak ground acceleration (PGA), characteristic intensity (Ic), acceleration that accounts for up to 95% of the arias intensity (A95), root-mean-square of acceleration (Arms), and sustained maximum velocity (SMV) are the IMs that yield the most advantageous and accurate predictions for PWP. In contrast, PWP exhibits a weak correlation with the predominant period (Tp), mean period (Tm), PGVmax/PGAmax, and maximum displacement. In comparison to low-frequency (LF) ground motions, high-frequency (HF) ground motions tend to generate more significant site responses and lead to increased pore water pressure (PWP) in near-surface soil layers. HF motions lead to higher levels of spectral acceleration at the short-period and lower levels at the long-period.