The amethyst and agate geodes from the Los Catalanes Gemmological District in Uruguay represent one of the main deposits of its kind worldwide. The geometry of the deposit is horizontal, with an irregular distribution of amethyst geodes within the upper level of the basalt lava flows and shows strong variations in their abundance, as well as quality, geometry, and shape. Reliable exploration guides are scarce, and the limited knowledge of the geological parameters controlling its occurrence makes exploration unpredictable, leading to inaccurate reserve estimation. Based on cutting-edge methods including nucleation-assisted microthermometry of one-phase fluid inclusions and determination of triple oxygen isotope in silicates and carbonates, as well as analysis of geode-hosted water and groundwater, we estimate the crystallisation temperatures in the range between 15 and 60 °C. These low temperatures point to amethyst crystallisation after the emplacement of the complete basalt pile. The mineralising fluid shows isotopic signatures consistent with meteoric water and very low salinities from pure water up to rarely over 3 wt% NaCl-eq., likely sourced from the groundwater hosted in the aquifers in the basaltic sequence and underlying units. Based on the insights provided by the new data, we propose the combination of open- and closed-system crystallisation inside pre-existing cavities due to the episodic infiltration of meteoric water in a rather stable geological context.