Water quality plays a vital role in determining the sustainability, safety, and usability of a water source. Nutrient concentrations are among the primary indicators that determine and affect water quality. Understanding the factors that influence nutrient dynamics in watershed water bodies is crucial for effective nutrient management in watersheds, but the mechanisms underlying nutrient variation in streams versus small reservoirs remain incompletely resolved for this national strategic water source area for the the Middle-Route of the South-to-North Water Diversion Project of China (hereafter "the Middle Route"). This study conducted eight seasonal sampling campaigns across 65 streams and 23 small reservoirs within the Danjiangkou Reservoir watershed, the water source area of the Middle Route. By integrating catchment characteristics and water physicochemical parameters and applying model-averaging multiple linear regression (ΔAIC <2), we investigated the key catchment-scale and in-situ drivers of dissolved total nitrogen (DTN) and total phosphorus (TP) concentrations in these waterbodies. Results revealed that DTN and TP concentrations were significantly higher in spring and summer than in autumn and winter, likely driven by the combined influence of agricultural practices and hydrological processes. Multiple regression models showed that DTN was primarily influenced by soil total nitrogen (STN, -), water pH (-), and edge density (ED, -) (adjusted R2 = 0.28), with water physicochemical parameters explaining the largest portion of variance in streams (60.4 %). In reservoirs, DTN was mainly regulated by dissolved oxygen (DO, -) and STN (-) (adjusted R2 = 0.27). For TP in streams, turbidity (+), slope (+), and contagion index (CONTAG, -) were the dominant drivers (adjusted R2 = 0.30), whereas in reservoirs, TP concentrations were mainly associated with turbidity (+) and soil total P (STP, -) (adjusted R2 = 0.37). These findings highlight distinct nutrient regulation mechanisms in lotic and lentic systems, highlighting the need for seasonally adaptive management strategies. For streams, prioritize riparian buffer restoration and higher landscape aggregation (higher CONTAG, β = -0.39, p < 0.01) to intercept nutrients, and reduce fertilizer inputs during high-flow seasons. For small reservoirs, emphasize erosion control, turbidity reduction (β = 0.34, p < 0.001), and oxygen management (β = -0.49, p < 0.001), while minimizing fertilizer inputs to limit in-reservoir accumulation.