In the Next Generation Attenuation West2 (NGA‐West2) project, a 3D subsurface structure model (Japan Seismic Hazard Information Station [J‐SHIS]) was queried to establish depths to 1.0 and velocity isosurfaces for sites without depth measurement in Japan. In this article, we evaluate the depth parameters in the J‐SHIS velocity model by comparing them with their corresponding site‐specific depth measurements derived from selected KiK‐net velocity profiles. The comparison indicates that the J‐SHIS model underestimates site depths at shallow sites and overestimates depths at deep sites. Similar issues were also identified in the southern California basin model. Our results also show that these underestimations and overestimations have a potentially significant impact on ground‐motion prediction using NGA‐West2 ground‐motion models (GMMs). Site resonant period may be considered as an alternative to depth parameter in the site term of a GMM.