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Recent anthropogenic climate change and the exponential increase over the past few decades of Saharan dust deposition, containing ecologically important inputs of phosphorus (P) and calcium (Ca), are potentially affecting remote aquatic ecosystems. In this study, we examine changes in cladoceran assemblage composition and chlorophyll‐a concentrations over the past ~150 years from high‐resolution, well‐dated sediment cores retrieved from six remote high mountain lakes in the Sierra Nevada Mountains of Southern Spain, a region affected by Saharan dust deposition. In each lake, marked shifts in cladoceran assemblages and chlorophyll‐a concentrations in recent decades indicate a regional‐scale response to climate and Saharan dust deposition. Chlorophyll‐a concentrations have increased since the 1970s, consistent with a response to rising air temperatures and the intensification of atmospheric …