Bedrock mapping is essential for understanding seismic amplification, particularly in sediment-filled valleys or basins. However, this can be hard in urban environments. We conducted a geophysical investigation of the sediment-filled Bolzano basin in Northern Italy, where three valleys converge. This study uses low-impact, single-station geophysical methods suitable for urban areas to address the challenges of mapping in such environments. A dataset of 574 microtremor and gravity measurements, along with three seismic reflection lines, allows for the inference of the basin’s deep bedrock morphology, even without direct stratigraphic data. The dataset facilitates a detailed analysis of the spatial patterns of resonance frequencies and amplitudes, revealing 1D and 2D characteristics of the resonances. Notably, 2D resonances predominate along the Adige valley, i.e., the deepest part of the basin with depths up to 900 m. These 2D resonances, which cannot be interpreted through simple 1D frequency-depth relationships, are better understood by integrating gravity data to develop a depth model. The study identifies resonance frequencies ranging from 0.27 to over 3 Hz in Bolzano, affecting different building types during earthquakes. Maximum resonance amplitudes occur at lower frequencies, specifically at 2D resonance sites, therefore primarily impacting high structures. The 2D resonances are directional, with the most significant amplification occurring longitudinally along the valley axes. The resulting 3D bedrock model aids in seismic site response modeling, hydrogeological studies, and geothermal exploration and provides insights into the geological history of the basin, highlighting the role of the Adige Valley as a major drainage pathway.