Socially-relevant and controversial topics, such as water issues, are subject to differences in the explanations that scientists and the public (herein, students) find plausible. Students need to be more evaluative of the validity of explanations (e.g., explanatory models) based on evidence when addressing such topics. We compared two activities where students weighed connections between lines of evidence and explanations. In one activity, students were given four evidence statements and two models (one scientific and one non-scientific alternative); in the other, students chose four out of eight evidence statements and three models (two scientific and one non-scientific). Repeated measures analysis of variance (ANOVA) showed that both activities engaged students’ evaluations and differentially shifted students’ plausibility judgments and knowledge. A structural equation model suggested that students’ evaluation may influence post-instructional plausibility and knowledge; when students chose their lines of evidence and explanatory models, their evaluations were deeper, with stronger shifts toward a scientific stance and greater levels of post-instructional knowledge. The activities may help to develop students’ critical evaluation skills, a scientific practice that is key to understanding both scientific content and science as a process. Although effect sizes were modest, the results provided critical information for the final development and testing stage of these water resource instructional activities.