This research develops a Web‐based argumentation system named the Web‐based Interactive Argumentation System (WIAS). WIAS can provide teachers with the scaffolding for argumentation instruction. Students can propose their statements, collect supporting evidence and share and discuss with peers online. This research adopts a quasi‐experimental design, applying WIAS to the teaching of environmental issues, including mudslides, global warming and nuclear power. Fifty‐seven elementary school fifth graders from two classes participated in this research. With each class as a unit, they were divided into the WIAS group (n = 30) and the traditional argumentation instruction (TAI) group (n = 27). Before research, all students took the pre‐test of the ‘achievement test for environmental issues (ATEI)’ and the ‘environmental literacy scale (ELS).’ Then all students received argumentation training and six classes of argumentation instruction. Students in the WIAS group performed argumentation in the WIAS, while those in the TAI group performed argumentation in a traditional classroom. After the six‐class argumentation instruction, all students took the post‐test of the ATEI and ELS. The results show that students in the WIAS group have significantly better learning effectiveness than those in the TAI group. Students in the WIAS group also exhibited significantly better improvement in their environmental literacy.