Singapore is dedicated to developing geothermal resources to meet rising energy demand and achieve net-zero emissions by 2050. While above-average heat flow and local hot springs suggest high geothermal potential beneath Singapore, the associated deep thermal sources remain underexplored due to a limited understanding of the subsurface structure. Applying ambient noise tomography and converted/reflected body-wave imaging to new seismic data from North Singapore reveals a highly fractured, fluid-saturated shallow geothermal reservoir located southeast of the Sembawang Hot Spring in the Yishun district. This reservoir exhibits low Vs (< 3.2 km/s) and high Vp/Vs (> 2.1). At a greater depth of ∼4 km, a crustal seismic discontinuity indicates a transition from the upper Bukit Timah Granite to the porous metasedimentary basement, where a deep aquifer might form, supplying the shallow reservoir and, ultimately, the Sembawang Hot Spring through the fault and fracture system. Our results highlight Yishun as a potential site for deep drilling in future geothermal explorations, and more broadly, provide new insights into the deep heat sources of numerous medium-to-low enthalpy geothermal sites throughout the Southeast Asian batholiths.