To reveal the spatiotemporal evolution patterns and influencing factors of backwater effect of runoff in the lower reaches of the Ganjiang River, a hydrological runoff model suitable for plain river network areas was constructed and spatiotemporally coupled with a self-developed two-dimensional hydrodynamic model. The coupled hydrological-hydrodynamic model was adopted to simulate the backwater effect in the lower reaches of the Ganjiang River. Based on the simulation results, a water level difference prediction model was further established through multivariate regression analysis. The results show that the backwater effect in the lower reaches of the Ganjiang River is closely related to the discharge at Waizhou Station. During low-flow periods, the backwater in the north branch elevates the water level at Nanchang Station, while when the discharge increases, the spiral flow in the main branch propagates downstream, generating a backwater effect between Changyi and Nanchang stations. When the discharge exceeds the critical threshold of 513 m³/s, the water level of Poyang Lake is higher than that of the lower reaches of the Ganjiang River, initiating a backwater effect from the lake onto the river. When the discharge further increases to 3211 m³/s, the backwater effect dissipates, and the flow diversion between the East River and West River tends to stabilize. The rainfall-induced runoff influences the evolutionary process of the generation and recession of the backwater effect, with a retardation effect ranging from 12% to 19%. After incorporating a correction term of rainfall-induced runoff, the precision of the water level difference prediction model is improved.