Reservoir bays, which are affected by the reservoir and watershed characteristics, are the initial and most sensitive areas in the evolution process of reservoir water quality. However, the relationship between the watershed characteristics and nitrogen and phosphorus concentrations in reservoir bays is poorly understood. We selected 66 bays from the Danjiangkou Reservoir and sampled twice per year (storage and discharge periods) from 2015 to 2018 to monitor the total nitrogen (TN) and total phosphorus (TP) concentration in the waterbodies of the reservoir bays. Four types of watershed characteristic indices (topographic variables, soil variables, land-use composition, and landscape patterns) around these bays were obtained. We quantified the relationship between the TN and TP concentrations and watershed characteristics in the waterbodies of the reservoir bays using partial least squares regression (PLSR). The results showed that the mean concentrations of TN and TP in the storage period (TN:1.69 mg·L, TP:0.088 mg·L) were higher than those in the discharge period (TN:1.22 mg·L, TP:0.063 mg·L). The optimal PLSR models explained 67.9% and 82.5% of the TN concentration variability, and 65.4% and 67.2% of the TP concentration variability during the storage and discharge period, respectively. Based on the variable importance in the projection (VIP) values, soil erodibility had significant effects on the TN and TP concentrations. The key factors affecting the TN concentration were the slope gradient, basin relief, topographic wetness index, forest and agricultural land use, whereas the factors controlling the TP concentration were the landscape shape index, edge density, Shannon's diversity index and grass land use, although the TP concentration was also controlled by the patch density and contagion during the storage period, and by mean patch size and largest patch index during the discharge period. This study provides critical insights into sustainable landscape planning and effective reservoir water quality management.