Absorbent Biofilter Systems (ABS), composed of an anaerobic septic tank, a pump chamber and an absorbent biofilter tank, have been found to economically provide rural on-site wastewater treatment. This study was conducted to assess the potential of ABS effluent as an alternative water resource for agricultural and environmental use, with respect to the removal of pathogenic microorganism and their fertilization effect. A pilot scale ABS was used to compare its removal efficiency of pathogens from effluent water. Overall, more than 95 percent of Salmonella and E. coli were removed. This result demonstrates that a significant reduction in the pathogenic microorganism of effluents can occur in ABS, which implies the feasibility for the use of ABS effluent in agriculture and environment, with the provision of a further simple disinfection step, in order to satisfy the WHO guidelines for the microbiological quality in agriculture. In addition, because of the abundant nutritional content of ABS effluent, the substitution effect of fertilizer (N, P and K) in paddy irrigation, i.e. 2/3 for nitrogen, l/3 for phosphorus and 1/5 for potassium would be expected. Based on the experimental data, the ABS effluent could be used as a new alternative water resource for paddy irrigation, as well as for environmental purposes, such as supplying water to ecological parks in rural villages.