Recently, absorbent biofilters, which are inexpensive and easy to manacle, have been supplied to the rural areas, but have limitations in removing the nutrients effectively. Accordingly, as an alternative plan. natural zeolites were arranged in front or at the rear of the absorbent biofilters, and their removal efficiency for nitrogen and, ultimately, their applicability to the on-site wastewater treatment system were studied. Furthermore, the same experiments were carried out on artificial zeolites, made from coal ashes at National Honam Agricultural Experiment Station, to compare natural zeolites with artificial ones. Treated wastewater through the Absorbent Biofilter showed 22.6% nitrogen removal efficiency, while 64.6% was attained when natural Zeolites were placed in front of the absorbent biofilters (Zeolite-Aerobic process). As an addition, phosphorus was also efficiently removed. On the other hand, Aerobic-Zeolite process, which arranged natural zeolites at the rear of the biofilters, did not have significantly higher nitrogen removal as compared to the treatment using only the absorbent biofilters. Furthermore, upon regeneration of the natural zeolite, the ion exchange rate was fecund to increase over 10% as compared to before regeneration. Our results show that natural zeolites, applied to the on-site wastewater treatment system through the Zeolite-Aerobic process, not only increase the removal efficiency of nutrients, but, by choosing the appropriate regeneration time, can also be cast-effective. Artificial zeolites, on the other hand, though more efficient in removing nutrients, cannot be regenerated and, therefore, are not cost-effective.