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This dataset is the output of a NERC fellowship aimed to understand the long-term dynamics of tropical vegetation through palaeoecological analysis. For doing this, two sedimentary archives (Laguna Pindo and Laguna Baños) from Ecuador were radiocarbon dated and analysed for pollen, non-pollen palynomorphs, charcoal, chironomids, stable isotopes and XRF of tephra deposits. Each proxy was analysed at different resolution. Laguna Pindo is a mid-elevation lake (1250 m asl) that spans the last 50,000 years. Laguna Baños is an Andean lake located at 3800 m asl and contains sediments representative of the last 6500 years. Both water bodies are very shallow. The data is presented mainly in excel spreadsheets as raw data (except for radiocarbon dating data, which are the PDF files provided by NRCF and are available in the NGDC), without any math treatment or conversion (unless specified). NERC fellowship is NE/J 018562/1.