Rainfall-runoff and water flooding are the driving mechanisms of agricultural nonpoint source pollution (ANPSP), but existing research has hardly focused on water level–driven ANPSP. Danjiangkou Reservoir was the second largest reservoir in China, and its water quality was dominated by ANPSP. This study explored the effect of water level on water quality of Danjiangkou Reservoir and aimed to provide basis for water quality management of large reservoirs. The effect of water level–driven ANPSP on the concentration of reservoir ammonia was studied employing the methods of factor decomposition and multiple regression on a extensive time series data of reservoir ammonia, water level, rainfall, fertilizer usage, and inflow river ammonia. The long-term trend revealed the reservoir ammonia peaked in 2011 and the inflow river ammonia peaked in 2012 (Han River) and 2013 (Dan River), which indicated the success of point source control in the past 15 years and the dominant role of ANPSP in the reservoir ammonia in recent years. With the long-term trend series, the multiple regression results showed that 56% of the variation of the reservoir ammonia concentration was due to the water level (standardized regression coefficient 0.422), fertilizer usage (standardized regression coefficient 0.522), and inflow river ammonia (standardized regression coefficient 0.219). However, the rainfall was insignificant. The predominance of water level and fertilizer usage in explanation of the reservoir ammonia variation indicated that water level–driven ANPSP was the primary factor influencing the reservoir ammonia. The effect of water level was primarily reflected in the long-term variation of ammonia concentration rather than the seasonal variation within the year. This study showed that when compared with rainfall–driven ANPSP, water level–driven ANPSP had a greater impact on the reservoir ammonia. Water quality protection should center on the management of the water level–fluctuation zone.