To increase our understanding of long-term climate dynamics and its effects on different ecosystems, palaeoclimatic and long-term botanical reconstructions need to be improved, in particular in underutilized geographical regions. In this study, vegetation, (hydro)climate, and land-use changes were documented at two southeast Lithuanian peatland complexes – Čepkeliai and Rieznyčia – for the Late-Holocene period. The documentation was based on a combination of pollen, plant macrofossils, peat stratigraphic records, and subfossil trees. Our results cover the last two millennia and reveal the existence of moist conditions in Southern Lithuania between 300 and 500 CE and from 950 to 1850 CE. Conversely, changes towards warmer and/or dryer conditions have been recorded in 100, 600, and 750 CE, and since the 1850s. Significant differences with other Baltic proxies prevent deriving a complete and precise long-term reconstruction of past hydroclimatic variability at the regional scale. Yet, our results provide an important cornerstone for an improved understanding of regional climate change, i.e. in a region for which only (i) few detailed palaeobotanical studies exist and which has, in addition, been considered as (ii) an ecologically sensitive region at the interface between the temperate and boreal bioclimatic zones.