Selenium in the form of a reduced species such as selenocyanate is oxidized to produce an oxidized selenium species such as selenate or selenite, and then a biological reduction process is used to remove selenium from the oxidized selenium species. In an example, a chemical oxidant is added to a wastewater containing selenocyanate to produce selenate and selenite. The partially treated wastewater is then fed to a reactor containing a fixed media supporting a biofilm with selenium reducing organisms. The selenium in the selenate and selenite is reduced to an insoluble form of selenium, such as elemental selenium, which precipitates from the wastewater.