Pollen, non-pollen palynomorphs, charcoal and geochemical analyses of sediments from Lakes Salęt and Ruskowiejskie (NE Poland) were used to reconstruct vegetation changes in the former Galindia territory (Old Prussia) related to human activity and the climatic instability of the medieval period. Among archaeologists and historians, there is a widespread opinion that the permanent transformations of the environment in Prussia (south-eastern Baltic region) began not earlier than after its conquest by the Teutonic Order and resulted from its economic activity and intensive colonization. The impact of previous inhabitants of this land on the environment has been considered as definitely weak. Our results provide entirely contrasting evidence and demonstrate that strong and permanent deforestation started as early as in the early 11th century AD, in the pre-Teutonic Order time, and were associated with the economic activity of the Prussian Galinditae tribes. In this paper, we also discuss a possible interpretation of the medieval distribution patterns of Quercus. We assume that human activity catalysed and amplified both its spreading process and decline, primarily driven by the ‘Little Ice Age’ climatic deterioration. Our palynological results indicate the significant spread of Picea from ca. AD 1000, which we interpret as reflecting hydrological and climatic changes. Moreover, we hypothesize that the spread of Carpinus in the early medieval period (11th–13th centuries), which occurred in connection with more intense human activity, was largely because of woodland pasturing.