The Asal–Ghoubbet active rift in the Republic of Djibouti is a site of interest for geothermal energy and natural hydrogen, and previous studies have indicated that dihydrogen (H2) emanates from this rift. However, the well-known serpentinization reaction does not appear to be the main mechanism generating H2 at this site. Rather, the H2 is generated as follows: (1) by alteration of basaltic lava at depth via reaction with seawater flowing from Ghoubbet Bay towards Lake Asal; (2) by simple degassing of the volcanic chamber located a few kilometers below the Fiale Caldera in the rift axis; or (3) as a result of pyritization processes via the oxidation of H2S. Analysis of microorganisms did not indicate any production or consumption of H2, CO2, or CH4; therefore, it is unlikely that microorganisms affected H2 gas contents measured at the surface. However, air contamination at fumaroles is typically considerable and may limit interpretation of such processes. Drill cuttings from the Fiale 1 (F1) and Gale le Goma 1 (Glc1) wells (located on the inner and outer rift margins, respectively) were analyzed to determine where H2 is generated. Total rock analyses indicated distinct zones at depths of 464 m and 280 m for F1 and Glc1, respectively, representing the boundary between the Asal and Stratoïd Basalts. 57Fe Mössbauer analyses show a decrease in the percentage of Fe3+ at depth, indicating that Fe2+-rich material, particularly in the Stratoïd Basalts, may be a source of H2. Based on well data from the rift center and the outer rift margin, it is evident that H2 is present at the surface in the rift axis and that this area offers good remnant potential because of the presence of Fe-rich chlorite. Conversely, few H2 emissions were measured at the surface on the outer rift margins, although well data showed some H2 (~0.25%) at depth. The presence of a cap rock in the rift axis has not yet been proven; however, the high loss on ignition and the mineralogy in well Glc1 may indicate that the rocks are sufficiently altered to offer potential as a seal. If so, the rift margins would offer greater exploration potential than the rift center.