Kisima Ngeda (KN), a spring on the northern margin of saline Lake Eyasi, Tanzania, sustains an Acacia-Hyphaene palm woodland and Typha swamps, while the surrounding vegetation is semi-desert. To study the vegetation changes associated with this spring, which represents a plausible modern analog for the fossil springs documented in the nearby paleoanthropological and archaeological sites of Olduvai Gorge, we analyzed the pollen content of a 43 cm-long sediment core that documents vegetation changes since the last ~1200 years (from cal yrs. C.E. 841 to 2011). Our results show that (1) Hyphaene palms, which require meso-halophytic soil conditions were most abundant in the area of the coring site until cal yrs. C.E. ~1150 when the groundwater supplying the KN spring was likely lower than at present, allowing intrusions of saline lake waters. (2) From cal yrs. C.E. ~1200, a peat began to develop, the palm woodland was replaced by a Mimosaceae woodland, and the increased presence of Typha pollen indicates the presence of more wetlands. (3) From cal yrs. C.E. 1600, the groundwater level of the KN spring increased and reached its highest level in the last 1200 years. (4) Peaks of wetland expansion, which reflect increased groundwater flow and level in response to amplified rainfall in the recharge area (Mt Oldeani, Ngorongoro Highlands), occurred at cal yrs. C.E. ~1200–1400 and ~1650–2011. These outflows of groundwater at Kisima Ngeda were linked to the intensity and frequency of positive Indian Ocean Dipole (IOD) events, which trigger heavy rains in eastern Africa. We conclude that the Kisima Ngeda hydrological system, which has been active for more than 1200 years, responds rapidly to regional climate change driven by changes in the sea surface temperatures (SSTs) of the Indian Ocean. Yet, it is also capable of remaining active during dry intervals as inferred from the Kisima Ngeda record prior to cal yrs. C.E. 1200. Our results support the hypothesis that this type of system helped to maintain Plio-Pleistocene hominin populations and activities in the arid lowlands of the rift on a multi-decennial scale.