Purpose Understanding how archaeal communities are affected by water-table drawdown is essential for predicting soil functional responses to future climate change and the consequences of the responses on the soil carbon cycle. Material and methods We investigated the effect of watertable drawdown, warming, drought, and combinations thereof on archaeal communities using terminal restriction fragment length polymorphism (T-RFLP) and quantitative PCR.Results and discussion Methanosarcinales, Methanosaeta, Methanomicrobiales, Methanobacteriales, uncultured Rice Cluster II (RC-II), and uncultured Crenarchaeota were detected. Water-table drawdown and drought exhibited significant effects on the archaeal communities. When the water table was at or above 10 cm, the archaeal abundance at 10 cm remained high (approximately 10 9 cells per gram dry soil), whereas the archaeal abundance at 10 cm was reduced to approximately 10 8 cells per gram dry soil where the water table was lowered to 20 cm or below. When the water table kept constant, warming caused a significant reduction in the archaeal abundance, whereas drought only caused a decrease in archaeal abundance when the water table was higher than −20 cm. Conclusions Results suggest that changes in water table may directly impact archaeal community abundance and assemblage which can in turn influence methane emissions, potentially on a large scale. Our results also indicate that archaeal communities response to water-table drawdowns that are dependent on the initial ecohydrology.