Modeling is one of the core scientific and engineering practices described in A Framework for K-12 Science Education. Students are expected to construct, use, evaluate, and revise their models to make sense of phenomena or to find solutions to problems. Technology tools can support the development of students’ modeling practice when learning about environmental issues. This study investigates the incorporation of an online computational modeling tool in a middle school curricular unit focusing on ocean acidification. We present the advantages and challenges experienced by students and teachers while engaging in the unit and using the modeling tool. Our results indicate that integrating the modeling tool in the ocean acidification curricular unit facilitates students’ interest and engagement in environmental responsibility and focused students’ attention toward human involvement and impact on the environment. Students perceived the tool and the curricular unit to be relevant to their lives and important in promoting their content learning and modeling practice. However, students and teachers reported several challenges, mostly related to the complexity of using the modeling tool and working with the resulting graphs and charts. We discuss these advantages and challenges and suggest recommendations for supporting students’ modeling practice when learning about environmental issues.