In this study, an ecological impact was assessed for the short-term leak scenario through the AQUATOX-EFDC model, which combines the proven ecological model AQUATOX with the hydrodynamic model EFDC. A case study of the coupled AQUATOX-EFDC model was conducted for 30–30,000 kg toluene leak scenarios in the Jeonju River in South Korea. A 21-day scenario simulation was conducted, and the impact of the toluene spill accident was evaluated by comparing the biomass between the control simulation and the perturbed simulation. As a result of the simulation, it was found that in the scenario in which 3000 kg of toluene was leaked for a day, a substantial change was expected in the range of 0–640 m from the accident site. Additionally, for a 30,000 kg leak, a substantial change was expected in the range of 0–2300 m from the accident site, and the greatest damage was observed for the fish species group, the top predators. As a result, the AQUATOX-EFDC simulation showed a significant ecological impact, and the proposed model will be helpful to understand the ecological impact and establish the management strategy for the ecological risk of the chemical spill.