The use of alternative domestic wastewater treatment technologies such as constructed wetlands has gradually developed over the past 20 years. The present study aims at investigating a type of short-deep treatment constructed wetland beds BIOWATSYST to treat wastewater. Pathogenic bacteria and viruses are the most serious elements that contaminate domestic wastewater. The present study reveals that the BIOWATSYST system had a moderate efficiency to remove the load of pathogenic bacteria from the influent as Salmonella sp. (48%), Shigella sp. (52%), Vibrio sp. (49%) and Pseudomonas sp. (49%). Coliphages against Escherichia coli (RRL-3704) were isolated from the inlet and outlet water collected from the BIOWATSYST. The mean counts of these coliphages were 1357.5 pfu mL-1 in the influent, while their mean counts in effluents were 628.7 pfu mL-1. It was noticed that the mean bacteriophage counts of the influent against E. coli, Salmonella sp., Shigella sp., Vibrio sp. and Pseudomonas sp. isolates were in the range of (7-75 pfu mL-1). Also, the mean bacteriophage counts of the influent against Salmonella typhimurium (NCMB 74), Shigella boydii (ATCC 9207), Vibrio sp. and Pseudomonas aeruginosa (NCMB 8295) were in the range of (7-60 pfu mL-1). Very low counts of bacteriophages against bacterial isolates and bacterial test strains in effluents of all treatment beds were observed. Bacteriophages as a component of engineered wetlands received attention in the current study as indicators of pollution. When comparing somatic coliphages with classic bacterial indicators, it was noticed that there was a highly significant positive correlation between coliphages and all these groups of bacteria. These results may present confidant in the usage of coliphages as pollution indicator for secondary treated domestic wastewater. Furthermore the Addition of mixture of bacteriophages isolated from raw sewage resulted in the removal of 37% of fecal coliforms, while addition of high titer of coliphages resulted in the removal of 34%. Accordingly the ability these phages to eliminate their host pathogens from such systems is discussed.