We combined multiproxy analyses of plant sedaDNA, diatom, and lithological data from two sediment cores to develop an uninterrupted Lateglacial and Holocene record from the Dūkštelis palaeolake, eastern Lithuania, and compared our findings to published pollen records. SedaDNA provides localised and taxonomically detailed insights into vegetation, surpassing the resolution of pollen data; however, its composition is strongly influenced by aquatic plants, a fact which limits the representation of terrestrial flora to some extent. Macrophyte sedaDNA and diatom data record shifts in lake productivity and water levels, while pollen data reflect a broader regional vegetation context, highlighting the complementarity of these methods. Subalpine and lowland vegetation colonised the region during the Lateglacial. The presence of shrub taxa, like Arctostaphylos uva-ursi and Arctous alpina with colder-adapted species, like Dryadoideae and Pyrola, and herbs characteristic of lowlands in modern environments, like Trifoliaceae, Mentheae, Ranunculaceae, and Plantago, suggests an open but heterogenous environment with diverse microhabitats created under quickly changing geomorphological conditions. A gradual shift to a forested landscape began with the advent of riparian species like Alnus (∼11300 cal yr BP), Viburnum (∼10300–9200 cal yr BP), and deciduous trees including Ulmaceae, Tilia, and Fagaceae from ∼11150, 10000, and 9900 cal yr BP, respectively. Early to Middle Holocene diatom and macrophyte data show that by ∼10000 cal yr BP, the lake had shifted from a shallow mesotrophic-eutrophic state to a deeper eutrophic system. During the Middle to Late Holocene, sedaDNA data suggest a decline in forest vegetation as the lake evolved into a shallow wetland. At this stage, sedaDNA overrepresents species growing directly in and around the lake, and therefore potentially skewing the broader regional picture. In contrast, pollen data suggest a pronounced forest decline from ∼3300 cal yr BP, likely linked to human activities such as forest clearance, which would increasingly shape the landscape from the Middle Holocene. Notable agricultural and pastoral impacts are indicated by the presence of species such as Avena, Brassicaceae, Plantago, and Trifolium starting ∼3700 cal yr BP.