This paper presents a comprehensive palaeoenvironmental data set from Lake Skrzynka, northern Poland. A sediment core from the lake was investigated to reconstruct Lateglacial and Holocene environmental changes in northern Poland using a combination of palynology and stable carbon and oxygen isotope studies of carbonates and sediment geochemistry. The undisturbed sedimentation in Lake Skrzynka continues from the Allerød to the present. Our data suggest the persistence of dead ice in the Lake Skrzynka basin up to the Allerød. The sedimentary record of the lake reflects a considerable difference between the Lateglacial/early Holocene and the middle/late Holocene in terms of environmental conditions. The Lateglacial was characterized by rapid environmental changes, while climatic conditions throughout the Holocene were relatively stable. The trophic state of the lake was strictly dependent on climatically controlled vegetation changes and erosion tendencies in the vicinity of Lake Skrzynka. During the Lateglacial and early Holocene, as a result of predominantly open plant communities and enhanced nutrient export from the watershed, Lake Skrzynka experienced an increased trophy. The stabilization of forest cover and reduced input of nutrients resulted in the establishment of oligotrophic conditions in the lake in the early Boreal. During the late Subatlantic, the lake became eutrophic as a result of human disturbance of the local hydrological balance. The postglacial history of Lake Skrzynka can be regarded as representative of small, alkaline, through‐flow lakes in temperate climates.