A media bed reactor may be used to remove selenium from water. An exemplary reactor has a fluid injection system with one or more outlets located within the media bed. The fluid injection system may be connected to a source of gas, liquid or both. In a selenium treatment process, a denitrification zone forms above a selenium-reducing zone in the media bed. Operation of the reactor includes a step of flowing a fluid upwards through only an upper part of the bed. This upper part of the bed preferably contains at least most of the denitrification zone.