Data scarcity and uncertainty are the main limiting factors for an integral evaluation of the urban water and wastewater management system (WWMS) in developing countries. The present research shows an approach to use incomplete data sets to analyse the flows of water and nitrogen and to make an integral evaluation of the WWMS at a case study city. By means of data validation and model adaptations the use of literature values is kept at the minimum possible and so the current trends for water consumption and pollution in the city are identified. The material flows were calculated as central values with a certain confidence range and met the selected plausibility criteria. Thus, the first essential step needed to identify the challenges and opportunities of future improvement strategies at the WWMS of the city was possible.