Material flow analysis (MFA) and value flow analysis (VFA) were applied to the sanitation system in an urban slum in Indonesia. Based on the results of the MFA and VFA, garbage and excreta disposal costs were evaluated to be 0.7% and 1.1%, respectively, of per capita income. Such value flows seem reasonable in light of the recognized affordability to pay (ATP) standard. However, current excreta disposal methods create negative impacts on downstream populations. Because such disadvantages do not go back to disposers, but passed to downstream, the current value flow structure does not motivate individual toilet users to install treatment facility. Based on current material and value flow structures, a resource recycling sanitation system scenario was examined. Based on VFA, an affordable initial cost for such a system was calculated; this was found to be comparable in price to a cheaper composting toilet that is currently available in the market.