River migration and anthropogenic controls on hydrological processes may play important roles in estuarine system transformations and nutrient diffusion. We used a two-dimensional shallow water equation hydrodynamic water quality model to simulate total nitrogen (TN) transport under the situations of river migration and the “Water-Sediment Regulation Scheme” (WSRS). The results showed the following: (1) River migration changed the diffusion direction of high-TN-concentration water in the YRE from the east–west diffusion in 2009 to the north–south diffusion in 2019. (2) In the years the WSRS was active, the maximum diffusion distance of high-concentration-TN water is basically the same as that of the plume edge. In 2009 and 2019, it was 30 km in the southeast of the estuary and 26.5 km in the north. Concentrations of 0.5 mg/L and 1.05 mg/L in 2009 and 2019 can be used as the threshold for judging the farthest distance of diffusion. (3) In the years without the WSRS, the TN concentration in the YRE from June to July was generally lower than the same period in 2019, and the northward diffusion distance of high-concentration-TN water in 2017 was only 10% of that during the WSRS in 2019. (4) Runoff determines the diffusion range of TN in the YRE. The average runoff during the WSRS in 2019 was 6.88 times that of the same period in 2017, and the high concentration diffusion distance of TN in 2019 was 10 times that of 2017. Changes in estuary morphology determine the diffusion direction of nutrients. The results of this paper are helpful to further understand the nutrient diffusion law of estuaries and coasts under the influence of different factors, and to provide reference for the protection of water quality safety.