This research is aimed at developing a systematic and generally applicablemethodology for material flow analysis and integration in drain systems and watersheds.In particular, this research has focused on developing a mathematical framework andapplication for the management of nitrogenous species (primarily ammonium ions) inBahr El-Baqar drain systems and its outfall leading to Lake Manzala. Nitrogencompounds are among the most important species contributing to ecological cycles.Indeed, the environmental and biological aspects of water systems and their surroundingsystems are highly impacted by nitrogen compounds as they contribute to the quality,nutrition, and toxicity of these systems.In order to carry out the proposed research, a material flow model was developedto deal primarily with the water phase while including pertinent information on the solidand air phases as they interface with the water medium. Both spatial and discretetemporal dimensions were included to account for nitrogen flow and transformation. Themodel includes the various environmental phenomena that influence the fate andtransport of targeted species (e.g., volatilization, precipitation, sedimentation, uptake bybiota, adsorption, chemical and biochemical reactions, etc.). Furthermore, the modelincludes material flow analysis operators (or transfer functions) that characterize thesystem inputs and outputs as they relate to the surroundings. The aforementioned materialflow analysis tools were combined in a computer-aided modeling platform to provide acomplete material flow analysis and yield useful insights on the transport and fate oftargeted species. The simulation results shed insights on the system performance. Actualdata for the drain systems (Qalyoubia, Belbies, and Bahr El-Baqar) along with the outfallto Lake Manzala were used to illustrate the usefulness and applicability of the developedmodel. Comparison with the measured data confirmed the validity and fidelity of themodel.