Due mainly to climate change, it is apparent that serious waterborne diseases are emerging particular to those with inadequate sanitation systems. On the contrary, the conventional sanitation systems release significant amount of Green House Gas (GHG) unless proper operation and maintenance is undertaken. In this study, two scenarios have been proposed; 1) install biogas capture at offsite sanitation and 2) decrease number of cesspools by using septic tank to reduce GHGs emissions and risks. In term of microbial health risk, the direct reuse at offsite sanitation systems is still higher than the acceptable risk in both scenarios thus disinfection process is recommended. In order to achieve sustainable sanitation development, two strategies on GHGs emission and health risks reduction was proposed though four policies such as 1) capacities building for local authority, 2) provide suitable GHGs reduction and Health risk assessment practices, 3) enhance of social learning process on GHGs reduction and health risk assessment practices and 4) develop monitoring system should be provided to evaluate GHGs reduction and Health risk assessment practice for local authorities.