Summary Geophysics and Geotechnical Engineering commonly use one-dimensional (1D) wave propagation analysis, simplifying complex scenarios by assuming flat and homogeneous soil layers, vertical seismic wave propagation, and negligible pore water pressure effects (total stress analysis). These assumptions are commonly used in practice, providing the basis for applications like analyzing site responses to earthquakes and characterizing soil properties through inversion processes. These processes involve various in-situ tests to estimate the subsurface soil’s material profile, providing insights into its behavior during seismic events. This study seeks to address the limitations inherent to 1D analyses by using three-dimensional (3D) physics-based simulations to replicate in-situ tests performed in the Argostoli basin, Greece. Active and passive source surveys are simulated, and their results are used to determine material properties at specific locations, employing standard geophysical methods. Our findings underscore the potential of 3D simulations to explore different scenarios, considering different survey configurations, source types, and array sets.