Characteristics of waste and wastewater management can affect material flows. Our research investigates the management of waste and wastewater in urban areas of developing countries and its effects on phosphorus flow based on a case study in Hue Citadel, Hue, Vietnam. One hundred households were interviewed to gain insight into domestic waste and wastewater management together with secondary data collection. Next, a phosphorus flow model was developed to quantify the phosphorus input and output in the area. The results showed that almost all wastewater generated in Hue Citadel was eventually discharged into water bodies and to the ground/groundwater. This led to most of the phosphorus output flowing into water bodies (41.2 kg P/(ha year)) and ground/groundwater (25.3 kg P/(ha year)). Sewage from the sewer system was the largest source of phosphorus loading into water bodies, while effluent from on-site sanitation systems was responsible for a major portion of phosphorus into the ground/groundwater. This elevated phosphorus loading is a serious issue in considering surface water and groundwater protection.