Abstract: With the continuous advancement of environmental protection information and the constantly development of water environmental quality model，the demand to integrate water environmental quality model in water-environment management information system is becoming more and more urgent． This paper introduces the development history of EFDC model and its domestic application status，and presents the data structures of its multiple input documents． More importantly，with resort to EFDC-ML，a kind of makeup language on the basis of XML，this paper proposes a novel optimization method to reconstruct the various input documents of EFDC and optimize their original data structures，with the purpose of being adapted to the integration development of water-environment management information system．