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Mitigation of global warming scenarios by the United Nations Economic Commission for Europe (UNECE) water convention requires better water use policies by all management parties. One of Lisbon's municipal contributions to target a sustainable urban water cycle has been to assess the microbial and hydrochemical quality of groundwater. The aim is to clarify the possible existence of contaminations and respective sources, seasonality, and to assess non-drinking alternative uses of those waters. To this respect, five water sources over a 4-year period were monitored for physical, chemical, and microbial parameters (temperature, pH, NO2-, NO3-, NO4-, oxidability, conductivity, total hardness, Escherichia coli, total coliforms, enterococci, and heterotrophic plate count at 22 °C and 37 °C). The results show mean values of physical and chemical parameters within the WHO and national drinking water guidelines and regulations. However, microbial parameters exceed these limits, showing no seasonality. Microbial contamination may not necessarily imply the uselessness of groundwater for uses other than for drinking. For routine water quality assessment, a selection of a more adequate group of microbiological indicators is necessary, in order to evaluate potential public health risks, regarding the use of the identified water sources for non-potable purposes like irrigation or street cleaning. This approach is being promoted by the UNECE's protocol for water and health, article 6, 2 (i); in accordance with the scope of the UN's sustainable goals.