Based on the seasonal imbalance of water environmental capacity in Songhua River, the Harbin section of the main stream of the Songhua River was used as the research object, and the COD and NH3—N environmental capacity of Songhua River Harbin section was calculated using two-dimensional section-end model under dynamic hydrological design conditions. The results showed that the environmental capacity distribution of COD and NH3—N was uneven, and the environmental capacity distribution of COD was more unsatisfactory than that of NH3—N. The peak and valley value of the COD and NH3—N environmental capacity appeared in August and February respectively. As for different seasons, the maximum and minimum value of the COD and NH3—N environmental capacity appeared in flood season dry season respectively. The actual value of water environmental capacity was much lower than the ideal value, and the environmental pressure of NH3—N was more severe accordingly. The investigation results may serve as reference for efficient utilization of environmental capacity and water quality security in Songhua River.