Different polymers including tragacanth, vermiculite, perlite, silica gel and bacterial polymer were used to form biofilter for desalination. Salt tolerant Z1 bacterium was isolated from leachate and identified as Bacillus atrophaeus. It could produce high amount of exopolysaccharide with antifungal activity. The biofilters were made to contain several layers that include a thin layer of cotton, silica gel, tragacanth itself or tragacanth plus Z1 or Z1 exopolysaccharide, vermiculite and perlite. The biofilter included tragacanth itself had the capability to remove ammonium by 5% from 1 mM solution of NH 4 Cl. Adding Z1 bacterium to tragacanth, ammonium removal increased to 72%. Different salt solutions were exposed to certain amounts of alive Z1 bacterium, boiled Z1 bacterium and Z1 polysaccharide. Among them, extracted Z1 exopolysaccharide showed the most efficiently on the desalination of iron and cupper by 84.93% and 89.74%, respectively. Therefore, a synergistic effect of mixed Z1 exopolysaccharide with antifungal activity and tragacanth, to make biofilter were studied to remove different ions from salted well water. Our results have indicated that using Z1 polysaccharide and tragacanth in biofilter construction could effectively reduce Ca, Cl, Na, K, Pb, Cd and Zn from brackish well water. Using Z1 polysaccharide instead of Z1 bacterium prevents biofouling in biofilter construction. The different tests include UV-Vis spectroscopy, Fourier transform infrared spectroscopy (FTIR), X-ray diffraction and atomic absorption were used for relatively understanding the performed processes. FTIR analysis of Z1 polysaccharide itself, and with different salts showed interaction of Z1 polysaccharide functional groups, such as-OH,-COO and CO -C involved in different ions and metal biosorption process.