The tufa deposits in the Kurkur–Dungul area, southern Egypt, date from marine isotope stage (MIS) 11 to MIS 1. Springs across the region were active during glacial periods (with sea level below –50 m), reflecting changed atmospheric circulation over the Indian Ocean, as well as peak interglacial periods. During times of low sea level, reduced Indonesian throughflow promoted formation of an Indian Ocean Warm Pool, and anomalous rainfall on its western margin. We suggest Egypt lies at the intersection of westerly (“maghrebian”) and easterly (“mashriqian”) rainfall provinces, which show different timing with relation to orbital forcing and different source water regions. Tufa-growth periods are therefore not mechanistically linked to “humid periods” or “sapropel events” identified elsewhere. Stable isotope and TΔ47 data are also inconsistent with these spring systems being part of a larger system spanning northern Africa, and lack a clear interaction between northern hemisphere heating and mid-latitude rainfall. We also follow previous authors in concluding that formation of springline deposit formation was likely delayed compared to rainfall, due to aquifer flow distances. This delay is unlikely sufficient to explain why rainfall is out of phase movements of the monsoon belts, but may complicate interpretation of these records.