Lake Tzibaná is one of the largest (1.27 km2) and deepest (Zmax = 52 m) karstic lakes in the UNESCO’s Biosphere Reserve “Nahá-Metzabok” and in the Lacandon Forest, southeastern Mexico. It archives sediments from multiple sources and the inflowing Nahá River forms deltaic deposits. In 2019, the water level in Lake Tzibaná declined by ~ 15 m, persisting for 4 months and exposing the Nahá River Delta. A geophysical profile on the exposed delta revealed an accumulation of ~ 20 m of such deposits. Three sediment outcrops from an inactive channel in the Nahá River Delta, which ranged in height from 0.6 to 1.43 m, were sampled and a multi-proxy analysis of biological remains and geochemical variables was conducted. Four facies were observed: (1) massive-coarse sand, (2) fine sand, (3) dark leaf litter and (4) massive silty clay, each characterized by specific microcrustacean, testate amoebae and diatom taxa. Six dark leaf litter horizons were radiocarbon dated and revealed a complex depositional history including inverted ages making the establishment of an age model difficult. Nevertheless, past lake-level changes and the formation of the four facies match three characteristic water-level stages, which can also be observed on recent satellite images: (1) Massive-coarse sand deposits, with compositional and sedimentological characteristics of a shoreline environment and fluvial lateral banks, were formed during large-magnitude reductions in the lake level, similar to the one in 2019, (2) Interbedded layers of fine sand and dark leaf litter, currently found in low-energy fluvial environments, were formed during shorter and less pronounced decrease intervals, and (3) Massive silty clay, with distinctive microorganisms from low-energy lacustrine environments, is deposited during high water-level stages, when the delta is covered by water. Our findings illustrate how hydrological changes alter sedimentary dynamics in deltaic areas of lakes. Despite the complexity of their depositional processes, deltaic records can serve as a complementary source of paleolimnological information to records from distal zones due to their sensitivity to variations in water level, especially during extreme and prolonged desiccation events. Future research should attempt to combine evidences from deltaic and sediment sequences from deeper zones of Lake Tzibaná to reconstruct water-level variations during the entire Holocene. Understanding past lake-level reductions is not only relevant for the local indigenous communities but also crucial for the conservation of this ecosystem of international importance.