Water environmental capacity is an important factor in total pollutant control and water environmental management. Due to the uncertainty of the water environment, the uncertainty analysis of water environmental capacity is crucial. Most uncertainty analyses of water environmental capacity do not consider the correlation between various parameters that were used to calculate water environmental capacity. In this study, the copula model of discharge and water quality was constructed to analyze the uncertainty of water environmental capacity. The risk threshold of each river section was calculated when the water environmental capacity was less than 0 in the wet, normal and dry seasons. The Yitong River Basin in Changchun city was taken as a case study. The results showed that the 68.27% confidence level was considered to reduce the uncertainty of water environmental capacity by more than 54.90%. The uncertainty of water environmental capacity in the wet season was the largest, and the risk threshold was the smallest. The risk thresholds for the water environmental capacity of each river reach were all greater than 90% in the dry season. The method of this study can be extended to other basins for uncertainty analysis of water environmental capacity.