It is important to improve soil water effective storage for enhancing soil basic fertility. The long-term changes of water contents in soil profiles were studied by using a 10-year lysimeter experiment in an upland red soil under continuous maize cropping with manure application. The field experiment involved three treatments: no manure (CK), low-rate manure with N 150 kg/hm2 (LM), and high-rate manure with N 600 kg/hm2 (HM). The changes of volumetric water contents in soil profiles from 30cm to 100cm depth were observed from 2002 to 2011, and the relative impact of environmental and human factors (precipitation, air temperature and organic manure) on soil water variation was evaluated by aggregated boosted trees (ABT) analysis. The mean soil water contents in different depth of soil profiles were decreased in the sequence of wet years (0.389 cm3/cm3) >average years (0.380 cm3/cm3) >dry years (0.377 cm3/cm3). There was a significant logarithm regression relationship (r>0.582, P<0.05) between monthly precipitations and mean soil water contents in whole soil profiles (30–100cm) except for 2005 and 2009. Under the same manuring treatment, the mean soil water contents showed a significant difference among different soil depths in both cropping and fallow seasons of wet and average years, but not in the fallow season of dry years. The mean soil water contents in different soil depths were significantly but negatively correlated with the manure application rate, showing an increased soil water utilization with long-term manuring. Precipitation and air temperature were the dominant factors controlling the changes of soil water contents in the upper soil layers (30–70cm), which showed a relative impact of more than 80% by ABT analysis. However, the relative influence of precipitation on the soil water variation decreased with soil depth, while that of manure application increased. Manure application became the dominant factor controlling the soil water dynamics in the deep soil layer (100cm) during average and wet years.