An understanding of the morphological stability and succession of open water and wetland ecosystems in Nova Scotia is a priority for informing the conservation management of critical habitats for a complex of nationally listed, rare, disjunct wetland species. Baltzer Bog and Big Meadow Bog in southwestern Nova Scotia contain stratigraphic records of late Holocene moisture variability. Baltzer Bog is a shrub bog that formed in an elevated, enclosed kettle basin. Excavated sections exposed by peat mining revealed 2 distinct wood-rich horizons that are located above a well-developed soil and wood horizon that yielded a radiocarbon-dated age of 3260 cal. BP from an upright stump. The overlying wood-rich horizons were dated at 1640 and 1045 cal. BP and were overlain by Sphagnum species transitions indicative of increasing wetness. At Big Meadow Bog, a thin wood mat in Sphagnum at 90 cm depth was dated at 1760 cal. BP. These records are broadly correlative with pollen and stratigraphic data from Pleasant River Fen in central Nova Scotia that indicate periods of high and low productivity and a fluctuating water table from 1950 cal. BP until present. Though other high-resolution paleoclimate records from the region indicate that the late Holocene was a time of increasing precipitation and cooler air temperatures, these wetland records demonstrate that in Nova Scotia this time period was characterized by rapid variations in effective moisture and that significant and sustained dry periods likely occurred. This record of late Holocene moisture variability and its influence on habitat structure serves to better establish the potential for long-term residency of threatened and endangered species at wetland sites.