Under complex stratigraphic and morphological conditions, such as the ones typically occurring in basins, the realistic assessment of seismic site effects requires a refined, continuum-based modeling of the entire soil deposit. The effectiveness of the assessment is highly influenced by the assignment of boundary conditions. In this context, this paper presents the preliminary steps of a broader research path aimed at developing practice-oriented standards for basin effects under seismic loading. To this end, site response analyses are carried out on an example two-dimensional basin model using OpenSees and comparing the outputs of multiple boundary conditions techniques. Specifically, the following methods are employed along the lateral boundaries: kinematic constraints, Lysmer and Kuhlemeyer viscous absorbers, massive boundary columns and free-field boundary columns. The propagation of the seismic waves from the outcrop to the lower boundary is instead analyzed through a deconvolution procedure. Although preliminary, these results highlight some potentially relevant factors influencing the seismic performance of boundary conditions and suggest some practical indications about their applicability in boundary value problems.