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The volume of ocean environmental data is extremely massive, which makes it inefficient to manage them in standard ways. This paper promotes a new method to handle this problem. It presents a non-standard method that stresses on query-oriented organization of the data. Then it describes in details of the distributed management of the data based on the new relation schema design. The method has been implemented in a database cluster middleware named Distributed Ocean Environmental Data Manager (DOEDM). Experiments show that DOEDM gives a better support to the Marine and Atmosphere Geographic Information System (MAGIS) because it requires less storage space and has better query performance.