The role of argumentation processes to explain students’ science learning has been widely reported in the educational literature (e. g. Andriessen, 2006). The learning sciences have shown that collaborative classroom interaction can often contribute to individual argumentative discourse. Technology –especially computer-supported collaborative learning (CSCL) – has the potential to support productive argumentation. But many educational research studies have reported that most people have difficulties arguing collaboratively. The explosion of Web 2.0 technologies and social software accompanied by new affordances that expand communication, collaboration, learn and knowledge creation has opened a new era in education. This chapter departures from these arguments and will explore how to use the affordances of Web 2.0 technology to support science collaborative argumentation in secondary education. Special attention will be paid to the pedagogical features needed for a learning environment to use Wikis and scaffold students’ science argumentation processes. We begin the chapter by discussing argumentation theory and its implications in science learning. Second, we revise the educational possibilities of the Web 2.0 technologies, studying in depth the affordances of Wiki environments to enhance collaborative argumentation. Third, we continue by discussing the skills students will need to negotiate, discuss and to learn in a Wiki supported collaborative writing environment. Fourth, we study how to design a Wiki environment capable to scaffold argumentative skills. And finally, we report the pedagogical features used to design and implement a challenging Wiki learning environment. Specific scaffolds are provided to develop the main skills involved in science argumentation: elaboration, reasoning and reflection.