This study investigates the sources of water under four modes, namely, normal fields, Raised Fields, single agriculture in Raised Fields, and agroforest system in Raised Fields, by using a combination of δ 18 O, δ 2 H and δ 13 C and their effects on crop yield and water use efficiency. The results show that the soil electrical conductivity of Raised Fields during summer maize seasons was lower than that during winter wheat seasons, and that in the marginal regions was higher than in the central regions, because of the Water Sources. Under agroforest conditions in Raised Fields, Soil Salinity can be reduced because approximately 10% of the water originates from tree trunks. The biomass yield and intrinsic water use efficiency of winter crops under agroforest was 15.1% and 5.5% higher than that under single agriculture, respectively. Thus, soil salinization can be reduced and productivity can be increased by controlling the Water Sources in ecosystems.