<p>Poorly gauged basins characterize most of the world’s aquifers and pose considerable challenges to hydrologists globally. A lack of data on water-table elevation, spring discharge and meteorological data limit our ability to assess and study historical, current, and possible future groundwater flows and spring discharges. These limitations, and others, severely hinder our ability to better understand and sustainably manage water resources, especially under a changing climate. We use the trans-boundary Hermon Jurassic Aquifer (HJA), which supplies substantial amounts of groundwater to Syria, Lebanon and Israel, as a case study to showcase an approach to address such challenges. To overcome the large data gap, we constructed a conceptual hydrogeological framework of the HJA along with numerical modeling, using only limited spring discharge data. Our groundwater flow and solute transport modeling reproduce with notable accuracy the transient hydrographs of the main springs over several decades and the main spatial sulphate composition distribution. Furthermore, our models define recharge areas and storage volumes for each spring, delineate groundwater flow-paths, constrain the spatial and temporal HJA dynamics, and explain the cause for varying spring chemistry. We, thus, show the potential of this non-conventional approach to study poorly gauged aquifers worldwide, especially karstic and phreatic regions, and how significant hydrological insights can be revealed, overcoming lacking hydrological information.</p>