The Granada Basin is located in the southeast of Spain, in the central sector of the Betic Cordilleras, in an area of high seismic hazard in the Iberian Peninsula. This hazard is due, in part, to local ground-motion amplification effects that have been observed at various locations in this basin. In this work, we use the indirect boundary element method (IBEM) to compute the three-dimensional (3D) seismic response of the deep structure of the Granada Basin for incident P- and S-plane waves coming from the south. We have analyzed the results in both frequency and time domains, and for the range of frequencies that we have been able to compute (between 0 and 0.312 Hz), the most relevant site effects are the local amplifications produced inside the sediments. Generally speaking, the observed amplification patterns of the displacements for incident SH waves are the highest at those locations where the basin is deeper. For P and SV waves, the “snapshots” show the amplification effects of both radial and vertical components, when the direct waves cross the Granada Basin. The amplification levels, with respect to the amplitude of the incident wave, are not so large, because the impedance contrast between the sediments and the bedrock (equal to 2.45) is relatively low. Moreover, two perpendicular receiver profiles are used to analyze the wave propagation, and we have observed the propagation of phases that can be identified as surface waves along the two profiles. The Rayleigh waves propagate with more energy on the forward direction (from south to north) of the incident body wave.