This paleolimnological study aims to investigate how natural processes and anthropogenic land-use changes have affected sedimentary phosphorus (P) forms and primary producers in a small, temperate lake (Lake Fuglsø, Denmark) throughout the Holocene. Our multi-proxy approach uses pollen, X-ray fluorescence scanning, carbon (C) and nitrogen contents and stable isotopes, sequential P extraction, 31P nuclear magnetic resonance spectroscopy, pigments, diatoms, and plant macrofossils from a 14C-dated sediment record. We found three periods of human impact: (1) low disturbance from domestic grazing during the early/mid Neolithic (~3600 to ~2600 BC), (2) higher disturbance because of animal husbandry and some grain cultivation during the Late Bronze and Pre-Roman Iron Age (~800 BC to AD ~100), and (3) strong disturbance caused by domestic grazing, intensified crop cultivation and, in particular, by retting of fiber plants during the Middle Ages and Renaissance (AD ~1000 to ~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, aluminum, 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.