Scientists regularly evaluate alternative explanations of phenomena and solutions to problems. Students should similarly engage in critical evaluation when learning about scientific and engineering topics. However, students do not often demonstrate sophisticated evaluation skills in the classroom. The purpose of the present study was to investigate middle school students' evaluations when confronted with alternative explanations of the complex and controversial topic of climate change. Through a qualitative analysis, we determined that students demonstrated four distinct categories of evaluation when writing about the connections between evidence and alternative explanations of climate change: (a) erroneous evaluation, (b) descriptive evaluation, (c) relational evaluation, and (d) critical evaluation. These categories represent different types of evaluation quality. A quantitative analysis revealed that types of evaluation, along with plausibility perceptions about the alternative explanations, were significant predictors of postinstructional knowledge about scientific principles underlying the climate change phenomenon. Specifically, more robust evaluations and greater plausibility toward the scientifically accepted model of human-induced climate change predicted greater knowledge. These findings demonstrate that instruction promoting critical evaluation and plausibility appraisal may promote greater understanding of socio-scientific topics and increased use of scientific thinking when considering alternative explanations, as is called for by recent science education reform efforts.