The Central European area has been extensively studied using qualitative reconstruction techniques focusing on the development of peatlands in the past; however, research based on quantitative techniques is still lacking, especially in relation to highlands and mountainous areas. In this study, we focused on the hydrological changes and human-induced disturbances that affected two raised bogs from the Orawa-Nowy Targ Basin (Carpathian region): Puścizna Krauszowska and Puścizna Mała. We aimed to reconstruct the development of peatlands and changes in water table under different intensities of human activities. Two peat sequences from two different bogs, both possessing absolute chronologies based on high-resolution 14C dating, were examined in terms of pollen, non-pollen palynomorphs, plant macrofossils and testate amoeba records. We detected an asynchronous decrease in the water table level on the bogs that took place between the 4th and the 7th century ad, which occurred simultaneously with a global cold period ad 300–600 (Migration Period) in case of the Puścizna Mała bog. A concurrent but insignificant human impact on bogs was recorded. A distinct wet shift corresponding to the Wolf solar minimum (ca. ad 1280–1340) in Puścizna Mała was detected during ca. ad 1300–1350. The effect of this climatic event on bog hydrology is difficult to estimate because of the simultaneous human-induced deforestation. Drainage and substantial acceleration of peat extraction in the 19th and the 20th century ad led to the significant disturbances in peatland; however, these bogs were still susceptible to dry climatic events.