Propagation of long-period ground motion in sedimentary basins has been a subject of great interest among seismologists and engineers. Intense long-period ground motions consist primarily of surface waves that get trapped or generated locally as seismic energy travels through sedimentary deposits. In the present work, we investigate the propagation of surface waves in the basins of Kanto and Nobi in Japan, during three relatively recent events: The Mw 6.6 2004 Niigata Chuetsu, the Mw 6.6 2007 Chuetsu-Oki and the Mw 9.0 2011 Tohoku earthquakes. We identify the surface waves using a signal processing technique that detects their polarization characteristics, in the time-frequency space, using orthogonality relations among phase vectors. Then, by applying the “Normalized Inner Product” (NIP), regions of a particular type of polarization are delineated and filters are applied to isolate the associated surface waves, along with their direction of propagation. With our investigation, we attempt to follow the ‘flow’ of seismic energy as it approaches just outside the basins, and then how it evolves once inside the basin. Our analysis shows that the long period (<0.1 Hz) surface wave energy approaching the Kanto basin during the 2011 Tohoku earthquake consists of Rayleigh waves, and that part of the seismic energy is converted to Love waves. In a higher frequency range (0.1–0.5 Hz), prograde Rayleigh and Love waves were detected in selected areas such as the Chiba sub-basin and the Tokyo lowlands. Regarding the Nobi basin, we find that whereas the Rayleigh waves in the frequency range (0.1–0.5 Hz) radiated during the 2011 Tohoku earthquake strongly interact with the basin, the Rayleigh waves radiated by the Chuetsu events appear to propagate through the basin unaffected. This difference in basin response is attributed to the different azimuthal direction of incidence of the surface wave energy.