The Puga valley, in Ladakh, contains one of India's most prospective geothermal systems. Substantial geophysical and geochemical research has been conducted to characterise this system, though uncertainties regarding the subsurface reservoir's geometry and permeability structure remain a barrier to its development. In this contribution, we aim to fill some of these knowledge gaps by integrating new geological data and structural analyses with previously published geochemical and geophysical interpretations, and derive an integrated conceptual model of the geothermal system. Using digital outcrop techniques and field mapping, we identify and characterise several important structures (faults and foliations) that facilitate fluid flow in the otherwise impermeable Tso Morari gneiss. Petrological and field evidence for outcropping hydrothermally altered lithologies, may have formed in a geothermal system analogous to the active one, are also presented. Based on these observations and a simplified finite-element model, we suggest that tectonic and topographic stresses likely control reservoir architecture and connectivity. Lastly, we caution that geomorphological evidence for neotectonic movement on faults at Puga indicate the need for seismic hazard assessment prior to exploitation of the geothermal system, and identify potential parallels between Puga and the Yangbajing geothermal field in China.