Due to their tolerance of hydraulic and organic shocks, biological aerated filters (BAFs) have high filtration efficiency and are suitable for the treatment of complex and sanitary wastewater. In this study for the first time, natural media of date kernel from Bam city was used as the BAF reactor media and, at the end of the reactor, a meshing sand filter separated by a standard metal grid from the natural filter section was used. This can be considered innovations in the media and filtration. In this work, the actual effluent of the hospital wastewater treatment plant was employed as the inflow wastewater to the reactor, and its organic and inorganic parameters were measured before and after the treatment by the BAF reactor. Reactor effluent measurement was studied in two steps. In one step, the effluent from the backwashing was returned to the reactor and, in the other step, effluents did not return to the reactor, the comparison of which showed that the backwashing effluent return method had more removal efficiency. The backwashing process was also studied in three ways: bottom backwashing (TB), top backwashing (BB), and top and bottom backwashing (TBBS), to determine the amount of water consumed and to achieve the desired result. Finally, the TBBS method was selected as the optimal method. The effect of backwashing effluent return was evaluated on the results of the parameters. Concentration of most of the outflow parameters was less or in accordance with EPA standard 2012.