The impact climate and land-use changes have on the hydrological conditions in peat bogs and lakes is often complex, but of great importance for the carbon budget and biodiversity in these ecosystems. Links and feedbacks between raised bog water table depth, lake level, net precipitation, hydrometeorological indices, and radial tree growth have been studied and identified in the Rėkyva wetland complex, Lithuania. Moreover, several statistically significant correlations between raised bog water table depths, lake level, local river runoff, and tree growth were observed. The changes of raised bog water table, lake level, and tree growth show synchronous trends despite variations in the absolute values. Our results show decreasing water table in the Rėkyva wetland complex over the last 100 years, especially in the middle of the 20th century. This study also shows a potential for reconstructing water table fluctuations in wetland complexes using multi-indicator approaches. Our observations and reconstruction show consistency with several regional studies and reconstructions of moisture variations in Baltic raised bogs, at least for periods without strong anthropogenic influences.