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...