It is well established that site effects and the interaction between the structure and the ground play a significant role in the structural damage observed after major earthquakes. The latter fact, along with advancements in computation geomechanics, has made more common the use of numerical dynamic soil-structure interaction (DSSI) analyses, for instance with the finite element method, to assess the seismic behaviour of structures in major engineering projects. However, the generation of the input motion at the base of the numerical model might not be a trivial task, particularly when the adopted motion is specified at the top of a nonlinear soil deposit. In this case, one-dimensional frequency domain analyses are usually employed for deconvolution, where nonlinear behaviour is accounted for through the equivalent linear approach. However, if a complex nonlinear elastoplastic constitutive description is adopted to characterise the behaviour of the soil, the original motion will not be recovered at the surface because of the very different approaches for representing the behaviour of the soil. In this context, the paper addresses the application of a time-domain deconvolution procedure which allows us to consider the same nonlinear behaviour of the soil that is intended to be used in the numerical DSSI analysis. The methodology was applied to the Treasure Island site, in San Francisco, during the 1989 Loma Prieta earthquake, where significant site effects were identified. Results show that the evaluated procedure can satisfactorily generate an input motion for the numerical model such that the adopted surface spectrum is recovered when propagated through the nonlinear soil deposit.