The objective of this paper is to develop a systematic methodology for mass integration in drain systems and watersheds. Mass integration is a holistic approach to the tracking, transformation, and allocation of species and streams. The watershed and drain system is first discretized into reaches. The MFA model developed in part I of this work (Simulation and Application to Ammonium Management in Bahr El-Baqar Drain System) is used to describe the environmental phenomena that affect the fate and transport of targeted species and the operators that characterize the system inputs and outputs as they relate to the surroundings. Next, we develop an integration framework which encompasses sources, sinks, and interception technologies to aid in the development for nitrogen-management strategies. The simulation model was transformed into a synthesis model by introducing optimization variables and including models for the potential management strategies. The problem of minimizing negative environmental impact subject to technical, social, economic, and regulatory constraints was posed as a nonlinear optimization program whose solution identified and synthesized the most effective solution strategies. These mathematical models and management strategies were coded into a computer-aided tool using LINGO programming platform. The program can be readily modified to address a variety of cases. Tradeoffs and sensitivity analysis were established using the devised model. The devised framework was applied to an Egyptian drain system (Bahr El-Baqar) along with the outfall to Lake Manzala. The results of the case study provide solution strategies for nitrogen management along with their technical, economic, and environmental implications.
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