We used recordings of the M 6.8 Nisqually earthquake and its ML 3.4 aftershock to study site response and basin effects for 35 locations in Seattle, Washington. We determined site amplification from Fourier spectral ratios of the recorded horizontal ground motions, referenced to a soft-rock site. Soft-soil sites (generally National Earthquake Hazard Reduction Program [NEHRP] class E) on artificial fill and young alluvium have the largest 1-Hz amplifications (factors of 3-7) for both the mainshock and aftershock. These amplifications are correlated with areas of higher damage from the mainshock to major buildings and liquefaction. There are several indications of nonlinear response at the soft-soil sites for the mainshock ground motions, despite relatively modest peak accelerations in the S waves of 15%-22%g. First, the mainshock spectral ratios do not show amplification at 2-8 Hz as do the aftershock spectral ratios. Spectral peaks at frequencies below 2 Hz generally occur at lower frequencies for the mainshock spectral ratios than for the aftershock ratios. At one soft-soil site, there is a clear shift of the resonant frequency to a lower frequency for the mainshock compared with the aftershock. The frequency of this resonance increases in the coda of the mainshock record, indicating that the site response during the weaker motions of the coda is more linear than that of the initial S wave. Three of the soft-soil sites display cusped, one-sided mainshock accelerograms after the S wave. These soft-soil sites also show amplification at 10-20 Hz in the S wave, relative to the rock site, that is not observed for the aftershock. The cusped waveforms and 10-20-Hz amplification are symptomatic of nonlinear response at the soft-soil sites. These sites had nearby liquefaction. The largest amplifications for 0.5 Hz occur at soft-soil sites on the southern portion of the Seattle Basin. Stiff-soil sites (NEHRP classes D and C) on Pleistocene-age glacial deposits display similar spectral amplification for the mainshock and aftershock, indicating approximately linear response. The stiff-soil sites generally have moderate amplification (factors of 1.1-2.4) at 0.5 and 1 Hz. Amplifications at 1 and 5 Hz for all sites generally increase with decreasing shear-wave velocity measured in the top 30 m (Vs 30). However, larger amplifications at 0.5 and 1 Hz for sites with similar Vs 30 values are observed for sites in the Seattle Basin, illustrating the amplification from the deeper (>30 m) sediments and the contribution from basin surface waves. Record sections for the mainshock and aftershock show that basin surface waves produce the peak velocities for many of the sites in the Seattle Basin and often dominate the amplitude at 1 Hz and lower frequencies.