Abstract: A two-stage treatment process, for the treatment of nitrate rich water, particularly aquaculture pond water, wherein in the first stage a degassing chamber is used for removing dissolved oxygen from a stream of water flowing out of the aquaculture system, and in the second stage the stream of water obtained from said degassing chamber is flown into a denitrifying biofilter comprising a biofilter media which functions as a biological growth media and as a carbon source, wherein said denitrifying biofilter is capable of biologically reducing both nitrate and nitrite compounds into nitrogen gas.