Mapping the soil-bedrock interface is crucial for tunnelling projects in engineering geology. This investigation demonstrates the effectiveness of a novel technique to calculate the horizontal-to-vertical (H/V) spectral ratio using ambient vibration measurements to characterize the unconsolidated sediment thickness and geometry of the top of the engineering bedrock in the city of Bilbao (northern Iberian Peninsula). Engineering bedrock is defined here as the consolidated rock layer underlying the Holocene sediments infill in the region. The non-invasive technique was integrated into the geophysical surveys conducted in 2019 for a subfluvial tunnel construction project beneath the Bilbao Estuary. We calculated the H/V transfer function at 37 sites using an AutoRegressive Moving Average (ARMA) model, which has been shown to be robust in extracting the ground fundamental resonant frequency with high spectral resolution. Lithological information from coincident stations and boreholes supports the empirical interpretation of the H/V spectral peaks in terms of peak impedance contrast depth. The estimated engineering bedrock exhibits morphological complexity with depths ranging from ∼10 m to ∼47 m below the surface. The obtained unconsolidated sediment thickness map is consistent with the geology known from the scattered historical borehole data and is supported by the results of the soil geotechnical characterization conducted in 2021 to advance the planning phase of the subfluvial tunnelling project. We show that the novel H/V approach used in this work is robust and yields somewhat higher resolution results than other commonly used H/V methods. The resolution of the method enables the use of H/V estimates to efficiently plan well campaigns and minimise costs, even for relatively shallow targets. We conclude that H/V mapping using this novel technique can help select layout alternatives in the early stages of tunnel construction planning, especially in heavily urbanized areas. •Engineering bedrock estimation in the Bilbao Estuary for a subfluvial tunnel project.•The H/V spectral ratio function is modelled using an ARMA filter.•Resonance frequencies are empirically compared to coincident borehole log data.•Maps of sediment thickness, ranging from 10 to 47 m, align with drill hole data.•H/V investigations can optimize geotechnical projects cost-effectively.