Dissolved organic matters and ammonia nitrogen are serious contaminants of surface water in Taiwan. These contaminants can interfere with the water treatment process and cause biological instability in the finished water. One solution is to employ a biological treatment stage prior to the conventional water treatment process. A continuous flow biological filter packed with reticulated PU foam was used to remove ammonia nitrogen and organic materials before the conventional water treatment practice. The effect of its operation mode, namely, empty bed contact time (EBCT) and backwash, on the removal efficiencies of ammonia and organic matter was examined. The results suggested that ammonia nitrogen and organic nitrogen can be effectively removed by controlling the operation mode of the biological fixed bed. Efficient ammonia nitrogen removal was achieved upon the combination of the backwash mode with short EBCT or extended EBCT without the backwash. Efficient organic nitrogen and DOC removals were observed at short EBCT without the backwash. This study provides insights into the function of biofiltration, which benefits the design of a fixed-bed bioreactor for the treatment of polluted surface water.