Ground motions in the Los Angeles Basin during large earthquakes are modulated by earthquake ruptures, path effects into the basin, basin effects, and local site response. We analyzed the direct effect of shallow basin structures on shaking duration at a period of 2–10 s in the Los Angeles region through modeling small magnitude, shallow, and deep earthquake pairs. The source depth modulates the basin response, particularly the shaking duration, and these features are a function of path effect and not site condition. Three-dimensional simulations using the CVM-S4.26.M01 velocity model show good fitting to the initial portion of the waveforms at periods of 5 s and longer but fail to predict the long shaking duration during shallow events, especially at periods less than 5 s. Simulations using CVM-H do not match the timing of the initial arrivals as well as CVM-S4.26.M01, and the strong late arrivals in the CVM-H simulation travel with an apparent velocity slower than observed. A higher-quality factor than traditionally assumed may produce synthetics with longer durations but is unable to accurately match the amplitude and phase. Beamforming analysis using dense array data further reveals the long duration surface waves have the same back azimuth as the direct arrivals and are generated at the basin edges, while the later coda waves are scattered from off-azimuth directions, potentially due to strong, sharp boundaries offshore. Improving the description of these shallow basin structures and attenuation model will enhance our capability to predict long-period ground motions in basins.