The use of socio-ecological controversies, such as global warming, in classrooms has been suggested to increase students’ awareness about complex issues, although detailed analysis of their implementation in classrooms are still scarce. This research shows a model-based inquiry approach (MBI) instructional sequence, using scientific news as a trigger, aimed at addressing a global problem on a real socio-ecological system: the effect of global warming on the Great Barrier Reef. Its implementation in a lower secondary school classroom allowed the assessment of the effectiveness of the instructional sequence designed, based on students’ perception of what secondary school students have learned and felt. Results show that the MBI instructional sequence seems to have favored the mobilization of students’ alternative conceptions about global warming, coral reefs, and symbiotic relationships. In addition, it contributed to increasing the students’ awareness of the problem of global warming and its effects on an essential socio-ecological system, such as coral reefs.