The Three Gorges Project (TGP) has greatly enhanced the heterogeneity of the underlying surface in the Three Gorges Reservoir Area (TGRA), thereby affecting the hydrologic processes and water quality. However, the influence of the differences of underlying surfaces on the hydrologic processes and water quality in the TGRA has not been studied thoroughly. In this research, the influence of the heterogeneity of landscape pattern and geographical characteristics on the spatial distribution difference of hydrologic processes and water quality in the different tributary basins of the TGRA was identified. The TGRA was divided into 23 tributary basins with 1840 sub-basins. The spatial differentiation of the hydrologic processes and water quality of the 23 tributary basins was examined by the Soil and Water Assessment Tool (SWAT). The observed data between 1 January 2010 and 31 December 2013 were used to calibrate and validate the model, after which the SWAT model was applied to further predict the runoffand water quality in the TGRA. There are 25 main model parameters, including CN2, CH_K2 and SOL_AWC, which were calibrated and validated with SWAT-Calibration and Uncertainty Procedures (SWAT-CUP). The landscape patterns and geomorphologic characteristics in 23 tributary basins were investigated and spatially visualized to correlate with surface runoffand nutrient losses. Due to geographical difference, the average total runoffdepth (2010-2013) in the left bank area (538.6 mm) was 1.4 times higher than that in the right bank area (384.5 mm), total nitrogen (TN) loads in the left bank area (6.23 kg/ha) were 1.9 times higher than in the right bank area (3.27 kg/ha), and total phosphorus (TP) loads in the left bank area (1.27 kg/ha) were 2.2 times higher than in the right bank area (0.58 kg/ha). The total runoffdepth decreased from the head region (553.3 mm) to the tail region (383.2 mm), while the loads of TN and TP were the highest in the middle region (5.51 kg/ha for TN, 1.15 kg/ha for TP), followed by the tail region (5.15 kg/ha for TN, 1.12 kg/ha for TP) and head region (3.92 kg/ha for TN, 0.56 kg/ha for TP). Owing to the different spatial distributions of land use, soil and geographical features in the TGRA, correlations between elevation, slope gradient, slope length and total runoffdepth, TN and TP, were not clear and no consistency was observed in each tributary basin. Therefore, the management and control schemes of the water security of the TGRA should be adapted to local conditions.