[Objective] Danjiangkou Reservoir is the core water source of China’s South-to-North Water Diversion Middle Route Project, with a 378.82 km² water-level-fluctuation zone (WLFZ) where agricultural planting covers 45.39% of the 158-170 m area, threatening adjacent reservoir bay water quality. Existing studies lack clarity on region-specific planting impacts and risks from pathways like rainfall runoff and submergence. This study aimed to: (1) quantify total nitrogen (TN) and total phosphorus (TP) changes in soils and bay waters before/after planting and rainfall; (2) measure TN/TP release rates from soils under submergence via simulations; (3) provide targeted support for WLFZ water quality protection. [Methods] A total of 10 topsoil samples (0-15 cm) and 9 bay water samples (0.5 m below surface) were collected during pre-planting (Sept. 6-7, 2024), post-planting/pre-rainfall (Oct. 22-23, 2024), and post-planting/post-rainfall (Nov. 16-17, 2024). Soil TN/TP and water quality indicators were tested following national standards. Static immersion experiments used soil columns (5 cm height) with 2 L reservoir water, sampling every other day until concentration stabilization. [Results] (1) Soil TN concentrations rose by 159-890 mg/kg, with the mean value increasing from 790 mg/kg (pre-planting, mostly Grade Ⅴ-Ⅵ, low nutrient level) to 1 246 mg/kg (post-planting, mostly Grade Ⅲ-Ⅳ, medium level). Soil TP concentrations increased by 46-546 mg/kg, with the mean rising from 608 mg/kg (pre-planting) to 669 mg/kg (post-planting); only unfertilized sites showed no increase or a decrease. After rainfall, soil TN decreased by an average of 266 mg/kg (range: 80-698 mg/kg), with the largest drop (698 mg/kg) in Shengwan Town. Soil TP decreased by an average of 149 mg/kg (range: 58-332 mg/kg), with the largest decline (332 mg/kg) in Jiuchong Town.(2) Rainfall led to significant water quality deterioration: the proportion of Ⅰ-Ⅱ class water (per GB3838-2002) dropped from 88.81% (pre-rainfall) to 33.33% (post-rainfall). Water TN increased by an average of 14% (range: 0.07-0.47 mg/L). Water TP surged by an average of 255% (range: 0.01-0.10 mg/L). This indicated that TP (dominated by particulate phosphorus) was more vulnerable to rainfall erosion than TN.(3) Planting significantly enhanced TN and TP release from soils. Annual TN release rates increased by 65%-386%: from 16.1 mg/(m²·d) to 26.62 mg/(m²·d) (Jiuchong Town D2-166), 16.77 mg/(m²·d) to 81.51 mg/(m²·d) (Xianghua Town D1-166), and 7.36 mg/(m²·d) to 33.1 mg/(m²·d) (Cangfang Town D3-163). Annual TP release rates increased by 6%-232%: from 3.59 mg/(m²·d) to 3.79 mg/(m²·d) (Jiuchong Town D2-166), 0.38 mg/(m²·d) to 1.26 mg/(m²·d) (Xianghua Town D1-166), and 0.48 mg/(m²·d) to 1.10 mg/(m²·d) (Cangfang Town D3-163). Nutrient release followed a consistent pattern: rapid release in the early stage and gradual stabilization later, though release amounts varied significantly across different planting sites. [Conclusion] This study innovatively clarifies region-specific pollution risks and nutrient release of agricultural planting in the Danjiangkou Reservoir WLFZ. Agricultural planting increases soil TN/TP accumulation, while rainfall runoff and submergence accelerate their migration to water bodies—with TP more susceptible to rainfall erosion. The marked rise in nutrient release rates post-planting elevates water quality risks during WLFZ submergence. Targeted recommendations include: (1) strengthening intensive water quality monitoring in high-risk bays (Xianghua, Shengwan, Jiuchong Towns) during peak planting seasons (April-May, October-November); (2) implementing strict fertilizer controls and regular inspections in these key regions; (3) prioritizing measures to reduce particulate phosphorus loss and mitigate eutrophication. These findings fill gaps in region- and pathway-specific pollution risk assessments and provide critical support for safeguarding the South-to-North Water Diversion Project’s water quality.