To rational use water resources and prevent water-related issues in Songhua river basin, the water environment effect for the three water resources allocation scenarios in 2030 year was analyzed by a comprehensive index evaluation method. The scenarios were the traditional water quantity allocation mode (S1), the total water-used quantity constrained allocation mode (S2) and the joint allocation mode between water quantity and its quality constrained by the S2 (S3). The results show that: the water resources shortage is 6.6 ×108 m3 in the whole basin in S1, the water environment security degree is the basic safety and insecurity with the safety value of 0.64 to 0.73. In S2, the water environment security degree maintains higher than the basic security category with 0.7 safety value under the 8.7 ×108 m3 shortage of water resources in the whole basin. In S3, the security degree with 0.75 safety level value reach to a safety category, meanwhile, the water deficit ratio becomes relatively uniform in spaces, and the water quantity and quality were further improved. In general, the implementation of environment security evaluation for water resources allocation the can reveal well possible water-related problems, which is an optimal choice to prevent these problems