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Reconstruction of droughts before instrumental data series is a challenge. We explore the use of cladoceran-macrophyte relationships in the sedimentary sequence of a small lake, Lagunillo del Tejo, as a tool for infer-ring extreme climate conditions. This lake is a karstic sink hole situated in Iberian Ranges (Spain), which is very sensitive to rainfall variations. We analyzed cladoceran subfossils and plant macrofossils from cores whose bottom dates back to the 12th century. Cladoceran species were divided into four groups based on their habitat preferences. Graptoleberis testudinaria and Acroperus angustatus were most associated with aquatic plants. A concordance between the variation in the sedimentary profile of plant-associated cladocerans, macrophyte remains (Chara and Ranunculus subgenus Batrachium) and lake level was observed. The different zones resulting from constrained cluster analyses of both communities coincided and also with the reduced and oxidized zonation of the sediment cores. Both paleoecological proxies indicate the existence of four main dry periods during the last millennia (ca. 1200AD, ca. 1500AD, ca. 1900AD and last decades) causing the lowering of the lake level and consequently the drying up of the outer ring of macrophytes and the loss of plant-associated cladocerans. These arid periods alternate with wetter phases such as the interval from the last quarter of the 17th century to the first decade of the 18th century (corresponding to LIA). Our approach can be used to trace the hydrological past of similar systems.