Active seismic surveys are routinely employed by academia to study geological structure of the crust and upper mantle. Wavefields generated during these surveys are sampled at the receiver locations, but the wave‐paths traveled from a source to a sensor remains unknown. Although seismic acquisition layouts designed to investigate complex crustal‐scale environments are often two‐dimensional, the seismogram recorded at the receiver location represents information gathered along the three‐dimensional wavepaths that might offset from the 2D source/receiver profile along its transverse direction. This so‐called 3D‐effect distorts the results of 2D seismic imaging, which is unable to handle the out‐of‐plane propagation. Despite the numerous 2D seismic imaging case studies, the assessment of this issue is often overlooked. However, the problem exists ‐ especially for crustal‐scale profiles, where seismic energy propagates over distances of hundreds of kilometers and probes different crustal units. In this work we investigate the impact of 3D‐effect on the results of 2D velocity model building from the academic ocean‐bottom seismometer data. We show with polarization analysis how the 3D‐effect can manifest itself in the data domain. Using various scenarios of acquisition we evaluate the imprint of the out‐of‐plane propagation on the data and the results of full‐waveform inversion. We show that 2D velocity model building from the seismic profiles acquired in the complex geological setting can lead to wrong solution. Looking for the remedy to this issue we couple different configurations of acquisition geometries with 3D full‐waveform inversion that allow to handle the 3D effect and provide correct model reconstruction.