In this study, empirical site amplifications and S-wave velocity profiles for shallow and deep soils are estimated using earthquake ground motion records in metropolitan Manila, the Philippines. We first apply a spectral inversion technique to the earthquake records to estimate effects of source, path, and local site amplification. The earthquake data used were obtained during 36 moderate earthquakes at 10 strong-motion stations of an earthquake observation network in Manila. The estimated Q value of the propagation path is modelled as $54.6f^{1.1}$. Most of the source spectra can be approximated with the omega-square model. The site amplifications show characteristic features according to surface geological conditions. The amplifications at the sites in the coastal lowland and Marikina Valley shows predominant peaks at frequencies from 1 to 5 Hz, while those in the central plateau are characterised by no dominant peaks. These site amplifications are inverted to subsurface S-wave velocity. We, next, discuss the relationship between the amplifications and average S-wave velocity in the top 30m of the S-wave velocity profiles. The amplifications at low frequencies are well correlated with the averaged S-wave velocity. However, high-frequency amplifications cannot be sufficiently explained by the averaged S-wave velocity in the top 30 m. They are correlated more with the average of S-wave velocity over depths less than 30 m.