Material flow analysis (MFA) is an effective tool for waste management, but low- and middle-income countries lack essential data for MFA. This study proposed a simplified MFA (sMFA) utilizing local expert judgment (LEJ) and examining the impact of simplification on its uncertainty. A stochastic sMFA model was developed for nitrogen and phosphorus in urban Mandalay, Myanmar. This model was compared with the intensive MFA (iMFA) model employing intensive surveys for primary data collection. For the total loadings to the environment, the medians of the sMFA were higher by 3% and 11%, respectively, for nitrogen and phosphorus than those of the iMFA. The widths of the 80% confidence intervals of these loadings in the sMFA, normalized by those in the iMFA, were − 0.05 and − 0.11, respectively. The three largest flows to the environment were the same for the two models: on-site sanitation effluent/leakage, greywater, and industrial wastewater. Large median gaps between the models were observed for industrial wastewater, fecal sludge, and human excreta, associated with informal waste management, whereby LEJ did not work well. Overall, the sMFA demonstrated a good estimation of nitrogen and phosphorus flows with limited increase of uncertainty, still requiring focused attention on informal waste streams.Graphical abstractSupplementary InformationThe online version contains supplementary material available at 10.1007/s10163-023-01660-5.