Abstract: The purpose of the study is to explore the online initial allocation of various water pollutant emission permits. According to the characteristics of various water pollutants, the specified bidding language is designed base on the value of water environmental capacity. The bidding language can provide an accurate quotation for multiple units of different water pollutant emissions over time. Aimed at each enterprise needs for various combinations of emission permit, the mechanism design model for online auctions is developed. On the basis of the model, the winner determination process and payment calculation process are designed. Thus, the auction mechanism is generated. The mechanism makes allocation decision immediately as each bid is revealed online and without the knowledge of enterprises who will subsequently arrive. The allocation decision determines whether a certain combination is allocated for the enterprise. The mechanism makes payment decision before the enterprise leaves. The theoretical analysis shows that the mechanism not only can attract more enterprises to volunteer for the auction, but also can incentive each enterprise to declare his truthful arrival time, unit value of water environmental capacity and depart time. Compared with the effective allocation under complete information, the mechanism achieves good results in many aspects such as social welfare, transaction rate of enterprises and utilization rate of emission permits. The mechanism helps to make the fair and efficient initial allocation plan of water pollutant emission permits.