The Sahara was potentially wetter in the past during the warm African Humid Period. Although debated, this climatic shift has been suggested as a possible analogue for a future warmer climate. The reported presence of paleo-lakes is one of the main lines of evidence for wetter conditions. Even today, Saharan desert lakes occasionally fill following rare extreme rainfall events. However, due to the scarcity of in situ observations, little is known about the hydrometeorological conditions that lead to such lake-filling episodes. Here, we examine the meteorology and hydrology of lake-filling episodes at Sebkha el Melah, a typically dry lake in the northwestern Sahara, to quantify the relationship between rainfall, runoff, and lake filling. Using satellite remote sensing, we identify heavy precipitation events (HPEs) and associated lake filling, and analyse their atmospheric drivers and moisture sources using meteorological reanalysis data. We identified hundreds of HPEs between 2000 and 2021, yet only six resulted in measurable lake filling. We show that the effective runoff coefficient – commonly used in paleo-lake studies to infer past precipitation –varies across five orders of magnitude for these filling episodes, and is substantially lower than values often assumed in the literature. Based on these observations, we suggest that the initial filling and persistence of Saharan lakes may be related to changes in the intensity, frequency or synoptic pattern of HPEs, rather than a change to mean precipitation alone. These results provide new constraints for interpreting paleo-lake evidence from the African Humid Period and for assessing future changes in water availability in a warming climate.