Leakage occurs in rural water supply pipelines very often and its locating is quite demanding even for specialists, which could result in a poor operation efficiency of rural water supply projects and thus a low rural water supply guarantee rate. In view of this problem, the detection of leakage, as well as its prediction, is of great significance for the operation, maintenance, and administration of rural water supply projects. The traditional monitoring-warning systems for urban water distribution networks cannot be applied to rural water distribution networks, due to various limitations. Meanwhile, as with the traditional models, most new approaches based on machine learning such as the artificial neural network (ANN), probabilistic neural network (PNN), and statistical learning theory (SLT) do not fit rural water distribution networks much better, being unable to converge and force high-accuracy results with small sample sizes, which is a crucial demand to meet when dealing with rural water supply pipelines. Extreme gradient boosting (XGBoost), a model that specializes in small sample sizes and has a high generalization ability, was applied to a rural water supply project in Ningxia, China. In this study, a monitoring-warning system featuring both leakage locating and quantity estimation was established based on XGBoost. The accuracy and F1-score of the leakage locating model were 95% and 93%, respectively, while those of the leakage quantity model reached 96% and 97%, respectively. Furthermore, the pressure of monitoring stations could be obtained through the feature importance analysis enabled by XGBoost, which is essential for leakage warning. These results indicate that this system based on XGBoost could be a promising solution to the leakage issue in rural water supply projects, as a great inspiration for future developments in intelligent monitoring-warning systems, thus providing reliable approaches for the sustainable development of rural drinking water supply projects.