The present study incorporated a scaffolding decision making procedure on an authentic environmental socio-scientific issue and investigated how students' decisions are intertwined with their values. Computer-based activities provided necessary information and allowed for the consideration of multiple aspects of the issue, the study of the effects of every possible solution and the formulation and balancing of criteria. The optimization strategy for decision making was adopted. Data collection relied on 51 sixth grade students (11-12 years old). Open-ended written tests were given to students before and after the learning intervention with two tasks: application of the optimization strategy and a meta-reflection question explaining their decision. Children incorporated several criteria in the decision making process, however, what guided their decisions were the criteria which were given the greater weight. These criteria were connected with substantive arguments and were based on decisive values. Three value-driven patterns of decision makers were revealed: strong anthropocentric, weak anthropocentric and ecocentric. The ability of assigning weight in conflicting criteria is a cornerstone for the emersion of how values are interrelated with decisions. Values arise when preferences are in conflict and decisions are made by weighting alternatives in comparison to our preferences. In conclusion, students have to learn to develop solutions that represent a compromise between economic, ecological, and socioeconomic dimensions, which include establishing a value hierarchy. The ability to weight decision criteria and to disclose underlying value considerations may be an elaborate way to work with multifaceted socio-scientific issues.