In developing countries, many tons of valuable nutrients (mainly nitrogen (N) and phosphorus (P)) are lost as waste derived from daily life and agriculture. Nutrient load quantification is an early step for recognizing environmental pollution, and a basic requirement for planning environmental sanitation options. Material flow analysis (MFA) has been used in the environmental sector in many cities of developing countries. In Mandalay, under rapid urbanization, environmental problems have risen to an alarming level. In this study, a nitrogen and phosphorus flow model was developed with a focus on organic waste. The system boundary was five urban townships of Mandalay city and components included in the system were agriculture, livestock, industry, and household. Household surveys, and farmer, livestock owner and industry manager interviews were conducted along with collecting secondary data to develop the model. Results showed that 304 ton-N/year and 258 ton-P/year were discharged from household to the environment as food waste, excreta and greywater. Approximately 3,200 ton-N from on-site sanitation were also annually released to the environment as toilet effluent/leakage and fecal sludge. Animal manure (83 ton-N/year and 16 ton-P/year) and market waste (456 ton-N/year and 71 ton-P/year) were also observed as losses of valuable resources. Applying nutrients from animal manure, fecal sludge, and organic solid waste in the agricultural sector can reduce the pollution load to the environment, and reduce the chemical fertilizer demand in the city.