Abstract Aim To investigate the long-term changes in aquatic vegetation in a lowland, shallow lake, and to assess the relationship between aquatic vegetation and natural and anthropogenic catchment changes . Location Gundsømagle Sø, Zealand, Denmark: a shallow (mean depth 1.2 m), hypereutrophic lake (mean annual total phosphorus (TP) c. 700 g TP L−1) located in a predominantly agricultural catchment (88% cultivated land). The lake is presently devoid of macrophytes. Methods One hundred and forty-seven contiguous samples from a sediment core (taken in 2000) were analysed for macrofossil remains together with loss-on-ignition and dry weight. From an earlier sediment core (taken in 1992), 67 samples were analysed for pollen and the two cores were correlated using the ignition residue profiles. Core chronology was determined by 210Pb and 137Cs dating of the recent lake sediments, while older sediments were dated by pollen-stratigraphical correlation, as 14C dating proved problematical. Aquatic macrofossil abundance was used to reconstruct past changes in the lake's plant community and water-level. The contemporary catchment land-use change was inferred from sedimentary pollen data, and soil erosion to the lake was deduced from the minerogenic content of the lake sediments. Results The macrofossil record covers the last 7000 years, but aquatic plant remains were scarce prior to c. 1300bc. After this date the abundance of submerged and emergent macrophyte remains increased dramatically, paralleled by an increase in sediment minerogenic matter and non-arboreal pollen (NAP). Aquatic plant remains were abundant for more than 3000 years until the mid 1900s. Macrofossils of Linum usitatissimum (L.) (flax) and high pollen percentages of ‘Cannabis type’ (hemp) were recorded in periods between c. 1150bcand 1800ad. Main conclusions Our study suggests that, between c. 5000bcand 1300bc, the submerged plant community was confined to the littoral zone. From 1300bconwards , the submerged macrophyte vegetation expanded rapidly across the lake bed, presumably as a response to lake shallowing caused by a combination of climatic-induced water-level lowering and enhanced erosional infilling of the lake basin due to intensified anthropogenic activities in the catchment. The lake was meso-eutrophic and had an extensive and diverse aquatic flora for more than 3000 years, until the middle of the twentieth century. In periods between c. 1150bcand 1800ad, the lake experienced direct anthropogenic impact from retting of fibre plants (Linum and Cannabis). Over the last 200 years, erosional infilling of the lake basin increased drastically, probably as a result of agricultural intensification. In the twentieth century, the lake was strongly affected by nutrient enrichment from both point sources (sewage from built-up areas) and diffuse agricultural run-off which led to hypertrophic conditions and the collapse of the submerged vegetation c. 1950–60. The concept of ‘naturalness’ and the implications for lake conservation are discussed.