This palaeo data set consists of a Holocene record from a small, temperate lake (Lake Fuglsø, Denmark). It comprises radiocarbon (¹⁴C)-dating, pollen, X-ray fluorescence scanning, carbon and nitrogen (contents and stable isotopes), phosphorus (P) pools (from sequential P extraction and ³¹P nuclear magnetic resonance spectroscopy), pigment, diatom, and plant macrofossil data. Our multi-proxy palaeolimnological study aimed to investigate how natural processes and anthropogenic land-use changes have affected sedimentary P forms and primary producers. We found three periods of human impact: (1) low disturbance from domestic grazing during the Early/Mid Neolithic (~3600 – ~2600 BC), (2) higher disturbance because of animal husbandry and some grain cultivation during the Late Bronze and Pre-Roman Iron Age (~800 BC – AD ~100) and (3) strong disturbance caused by domestic grazing, intensified crop cultivation and, in particular, by retting of fibre plants during the Middle Ages and Renaissance (AD ~1000 – ~1700). Cultural eutrophication during the latter phase caused unprecedented changes in the lake, including altered species composition, high production and strongly accelerated sediment accumulation rates. Generally, catchment deforestation was related to elevated proportions of metal (iron, aluminium, calcium)-bound P forms in the sediment, while high tree cover correlated with elevated proportions of P forms associated with organic material (“organic” P, humic-bound P, refractory organic P) and loosely bound P. During phases with forest in the catchment, silicon (Si) inputs to the lake were insufficient and diatom frustules were mostly absent in the sediments. In contrast, diatoms thrived in the lake when the landscape was open and erosional Si influx was high. This study is the first to show long-term (~eight millennia) and recurring Si limitation of diatoms, a finding that may explain the absence of diatoms in sediment records of other sites too. In summary, human land-use with preceding deforestation accelerated the transport of nutrients and elements from the terrestrial to the aquatic environment, leading to substantial and irreversible changes in Lake Fuglsø. Our study is a good example of the tight links between catchment processes and lake status, indicating that catchment dynamics should be considered in lake restoration projects, particularly for lowland lakes with high catchment:lake area ratios.

The sediment core was taken from a platform at the centre of the lake, using Kajak, Russian and Usinger corers. All proxies were determined according to standard methods, as described in the “Material and methods” section of the associated article.

We provide an Excel file which contains all data needed to plot figures 2 - 5 as well as figures S1 - S7 of appendix S1. All data are raw data, except for scores of PCA (Principal Components Analysis) axes. PCAs were performed using the program R (package “vegan”) and data of phosphorus forms (accumulation rates and percentage data) and pigments (accumulation rates). Prior to PCAs, data were square-root transformed. Abbreviations used in the Excel file, are explained in the last sheet.