© 2022, The Author(s), under exclusive licence to Springer Nature B.V.The high seismicity and tectonic activity of the study area located in a near-fault region in Gölyaka, Düzce, results in a bedrock geometry highly complex in the sense of faulting and deformation. This makes this area very challenging in terms of a site response study that would aid seismic hazard assessment. This study develops a basin model to evaluate the site effects in the tectonically formed Plio-Quaternary fluvial sedimentary layers of the Gölyaka region. The selected site uniquely falls within the near-field domain of a section of the North Anatolian Fault System. To determine the presence of these lateral variations in the geology as well as the geometry of the basin over a wide area, surface seismic measurements and deep vertical electrical sounding along with geotechnical boring studies have been performed, and a 3D basin geometry model was developed. The basin model shows that the sediment thickness continues to a depth of approximately 250–350 m with an irregular geometry due to over-step faulting near the southern boundary of the basin. Consequently, this study confirms the spatial variations in the near-field area that depend on basin geometry, material heterogeneity, and topography, indicating dipping and nonuniform stratification in the velocity profiles. Furthermore, the conducted microtremor measurements were used to compare the natural periods of microtremor results, along with interpolated Vs profiles to validate estimated basin depths. In conclusion, this study indicates that a well-developed basin geometry that reflects the complex process associated with the characteristics of the near-fault region could be accurately and reliably determined by developing a 3D basin model to assess site response in an account for seismic hazard assessment studies.