Treating and reusing municipal wastewater for urban agriculture raises water productivity. This paper developed a methodology to quantify water flows and productivity of a proposed infrastructure including water supply, sanitation, wastewater treatment and water reuse for agriculture. The methodology consists in calculating the pathogen reduction achieved with wastewater treatment, designing a crop scheme for the irrigation with treated water, modeling irrigation requirements and quantifying water flows with mathematical material flow analysis. This methodology was applied for the current state and with the planned facility in semi-arid Namibia. This infrastructure has the potential to raise water productivity by +10% as household water use increases with improved sanitation. Compared to not reusing the water for agriculture, water productivity can be raised by +39%. This methodology allowed the consideration of the impact of facility user behavior on water flows and found that water productivity increases less than computed with a fixed wastewater inflow.