Fate and seasonal variations of α-hexachlorocyclohexane (α-HCH) were simulated using a dynamic fugacity model in Lake Chaohu, China. Sensitivity analyses were performed to identify influential parameters and Monte Carlo simulation was conducted to assess model uncertainty. The calculated and measured values of the model were in good agreement except for suspended solids, which might be due to disregarding the plankton in water. The major source of α-HCH was an input from atmospheric advection, while the major environmental outputs were atmospheric advection and sediment degradation. The net annual input and output of α-HCH were approximately 0.294 t and 0.412 t, respectively. Sediment was an important sink for α-HCH. Seasonal patterns in various media were successfully modeled and factors leading to this seasonality were discussed. Sensitivity analysis found that parameters of source and degradation were more important than the other parameters. The sediment was influenced more by various parameters than air and water were. Temperature variation had a greater impact on the dynamics of the model output than other dynamic parameters. Uncertainty analysis showed that the model uncertainty was relatively low but significantly increased in the second half of the simulation period due to the increase in the gas-water diffusion flux variability.