Sustainable Development Goals (SDGs) have motivated several projects and policies to improve sustainable development. Assessing the progress made in fulfilling these goals is challenging, particularly in specific cases like urban water systems, because applied methodologies are lacking. This research proposes a methodology for assessing progress using SDGs indicators. The methodology was validated by considering SDG6 and SDG12 in real urban water systems from knowing that progress or the influence of decision making on its improvement exists. Eight indicators were evaluated in 120 case studies worldwide, of which 24 water systems were located in Spain. The global results showed substantial progress and fair progress in four and two indicators, respectively. The results revealed the alignment between both assessments in Spain. This research contributes to benchmark an indicator's progress, which will facilitate the decision-making process as to whether measures should be taken to improve the fulfilment of SDGs.