The increases of industrial and technological development and human activities have disturbed the balance of natural nitrogen (N) circulation. These phenomena have induced that large amounts of N are to be present in excess in air, soil and water environment. We investigated the effects of excess of reactive nitrogen (Nr) compounds on soil and water environment ecosystems through literature and case studies, and suggested the strategy of mitigating the acidification in soil and water ecosystems. Nr moves to air, soil and water media, can be converted to different types, and interacts with other chemical compounds. As an efficient N management plan, the evaluation (application of monitoring and safety index) and the chemical restoration (research and development) of the acidification in soil and water environment ecosystems are required to minimize the effects of Nr as well as policies to regulate the various emission sources and amounts of Nr.