During the early and mid Holocene deep lakes existed in the Tibesti volcanic complex, the highest mountain in the Sahara, but it is still unclear why they formed. Here, we combine sedimentary data analyses, high-resolution climate modelling and water balance modelling to provide a quantitative and differentiated estimate of the mid-Holocene water balance of the Trou au Natron (Doon Orei) and Era Kohor crater lakes and to discuss the underlying atmospheric circulation. During the mid-Holocene, the Tibesti received at least an order of magnitude more precipitation than the surrounding plains due to strong orographic uplift of moist air masses, which were surprisingly brought in by north-easterly winds from the Mediterranean, not by the stronger West African monsoon from the south. This may explain differences in the water levels between the Trou au Natron in the north-western part of the Tibesti and the Era Kohor in the south-eastern, leeward part. Our analysis demonstrates the importance of orographic precipitation for evaluating the hydroclimate of the central part of the Sahara – a factor grossly underestimated in the global climate models commonly used for palaeo and future climate simulations.