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Building resilience to climate change in the Afrotropics hinges on accurately predicting the style and tempo of ecosystem responses. Paleoecological records offer valuable insights into vegetation dynamics, yet high-resolution data sets remain scarce in Africa. Here, we present a new radiocarbon-dated sediment core from Lake Tanganyika, capturing terrestrial ecosystem responses to hydroclimate variability and fire activity during the Common Era. Phytolith and macrocharcoal records reveal oscillations between grasslands and woodlands in the Zambezian miombo region, transitioning from “stable” to “unstable” states depending on fire disturbance levels. The expansion of grasslands was facilitated by reduced precipitation, increased fire activity, and ecosystem interactions. Our data sets provide new constraints regarding the timing and landscape responses within the Lake Tanganyika watershed to global hydroclimate changes, including the relatively dry Medieval climate anomaly (ca. 1000−1250 CE) and the two phases of the Little Ice Age. Cold and wet conditions, which favored tree encroachment, prevailed during the “early” Little Ice Age (ca. 1250−1530 CE), whereas drier conditions coupled with increased fire activity during the “main” Little Ice Age (ca. 1530−1850 CE) promoted the expansion of open grasslands. Significant changes in grassland-woodland communities were driven and modulated by hydroclimate and rapid ecosystem feedbacks. Fire activity served as both a disruptive force, facilitating the opening of landscapes and restricting the encroachment of trees, and a steadying control that promoted a grassland “stable state” in the tropical savannas surrounding Lake Tanganyika. Understanding shifting vegetation patterns throughout the Common Era offers valuable insights for developing biodiversity conservation strategies, sustainable land-use practices, and the maintenance of ecosystem services provided by miombo woodlands for millions of rural poor in the Lake Tanganyika basin. 

Middle and Late Holocene sediments have not been extensively sampled in Lake Tanganyika, and much remains unknown about the response of the Rift Valley’s largest lake to major environmental shifts during the Holocene, including the termination of the African Humid Period (AHP). Here, we present an integrated study (sedimentology, mineralogy, and geochemistry) of a radiocarbon-dated sediment core from the Kavala Island Ridge (KIR) that reveals paleoenvironmental variability in Lake Tanganyika since the Middle Holocene with decadal to centennial resolution. Massive blue-gray sandy silts represent sediments deposited during the terminal AHP (~5880–4640 cal yr BP), with detrital particle size, carbon concentrations, light stable isotopes, and mineralogy suggesting an influx of river-borne soil organic matter and weathered clay minerals to the lake at that time. Enhanced by the AHP’s warm and wet conditions, chemical weathering and erosion of Lake Tanganyika’s watershed appears to have promoted considerable nutrient recharge to the lake system. Following a relatively gradual termination of the AHP over the period from ~4640 cal yr BP to ~3680 cal yr BP, laminated and organic carbon-rich sediments began accumulating on the KIR. δ¹⁵N_bulk, C/N, and hydrogen index data suggest high relative primary production from a mix of algae and cyanobacteria, most likely in response to nutrient availability in the water column under a cooler and seasonally dry climate from ~3680 to 1100 cal yr BP. Sediments deposited during the Common Era show considerable variability in magnetic susceptibility, total organic carbon content, carbon isotopes, and C/N, consistent with dynamic hydroclimate conditions that affected the depositional patterns, including substantial changes around the Medieval Climate Anomaly and Little Ice Age. Data from this study highlight the importance of sedimentary records to constrain boundary conditions in hydroclimate and nutrient flux that can inform long-term ecosystem response in Lake Tanganyika.