This book is aimed at developing a systematic and generally applicable methodology for material flow analysis and integration in drain systems and watersheds. In particular, this book has focused on developing a mathematical framework and application for the management of nitrogenous species (primarily ammonium ions) in Bahr El-Baqar drain systems and its outfall leading to Lake Manzala.. Indeed, the environmental and biological aspects of water systems and their surrounding systems are highly impacted by nitrogen compounds. In order to carry out the proposed book, a material flow model was developed to deal primarily with the water phase while including pertinent information on the solid and air phases as they interface with the water medium.. Next, mass integration techniques were employed 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. These mathematical models and management strategies were coded into a computer-aided tool using LINGO programming platform.