Like other perialpine basins and glaciated margins, the Geneva Basin in SW Switzerland is characterised by buried tunnel valleys, which are elongated incisions widely attributed to subglacial meltwater erosion beneath continental ice sheets. However, an inclusive understanding of the geological control on the evolution of the glacial landscape concerning the associated tunnel valley network is limited in the Geneva Basin. The lack of high‐density and high‐quality subsurface data sets mostly hampers this. Here, we present an updated map of the top Molasse bedrock underlying the glacio–fluvial Quaternary deposit based on the integration of the newly acquired 180 km ² 3D seismic data set and pre‐existing 2D seismic and borehole data sets. A seismogeomorphological interpretation coupled with attribute analysis of the data set revealed a drastic change in the morphology of the bedrock when compared to previous interpretations. This is especially within the perimeter of the 3D seismic data, revealing an intricately well‐defined geometry of the tunnel valleys network mapped in the Geneva Basin when compared with earlier studies. The bedrock was eroded by four tunnel valleys now named Montbrillant–Aire la Ville valley, Thônex–Plan‐les‐Ouates valley, Versoix–Avully valley, and Petit Lac–Avusy valley, and (smallest–largest) mostly trending NE–SW, reaching a depth of ca. 250 m in the Geneva Bay area. The seismic data also portray structural controls related to faults on the deepening and alignment of segments of the tunnel valleys. The longitudinal profiles generated for the tunnel valleys show a markedly undulatory thalweg, with predominantly U‐shaped and some localised V‐shaped cross‐sectional morphology. This geometry indicates that incision processes operated across significant topographic gradients along the tunnel valley axis. This characteristic is consistent with a polyphase origin for the tunnel valley network, likely modulated by repeated episodes of subglacial meltwater catastrophically eroding the Molasse substratum. This was associated with successive glacial advance–retreat cycles of the Rhône and Arve glaciers. This study demonstrates the unmatched capability of 3D seismic data sets in resolving the configuration of buried Quaternary tunnel valleys within this peri‐alpine realm. Importantly, it shows that an updated Molasse bedrock depth and Quaternary isopach map is vital for groundwater management, geothermal energy, resource extraction, and infrastructure planning in the Geneva Basin.