In this study, the inactivation performance of units against pathogenic and biotoxin threats in a water treatment plant are studied. The assessment of assets and hazards of water treatment plant against each of threats are studied by the RAMCAP risk analysis. The experiments showed that the Aflatoxin was eliminated only by disinfection units. The reverse osmosis unit had high efficiency in removing Ricin, while the sand filtration had the lowest efficiency in removing biotoxins. The microbial analysis showed the total coliform bacteria, thermotolerant coliform and HPC index were increased slightly by increasing the incoming water's pH and turbidity, while their count were significantly reduced by increasing the free residual chlorine. Water temperature changes also had a minor effect on microbial indexes. The RAMCAP analysis is used to reduce the vulnerability of units against conventional threats by determining the risk values of the units and finally, the presence of practical solutions.