In this study, we designed a web-based learning environment about water resources to support students' socioscientific decision making. The purposes of the study were to analyze and compare undergraduate students' interdisciplinary thinking and decision making at the individual and collective levels. Individual students first completed the web-based learning unit at home, in which they needed to decide on a suitable location for building a dam. Then, they worked in groups, discussing, debating, and negotiating to reach a group decision. Individual interdisciplinary thinking and decision making were recorded by the web-based platform. Group discussions were audio- and video-taped. Interdisciplinary thinking was analyzed qualitatively based on the SEE-SEP framework. Decision-making approaches were examined and categorized into different proficiency levels. The results show that, compared to individual decision making, the students used more moral or ethical considerations and made more links to personal experiences when engaged in group discussion. Despite wider aspects being considered at the group level, some facets such as their beliefs, values, and experiences regarding science were not adopted in the arguments at either the individual or the group level. Although a few students were able to use compensatory strategies when making individual decisions, none of the groups employed compensatory strategies to reach a group decision. The comparison between individual and collective levels manifests that group discussions can facilitate interdisciplinary thinking. The deficiencies in the group decision making identified in the study such as lack of deep reflection and not using a refined decision-making strategy underscore the need to provide scaffolds for collective decision making.