The purpose of this research was to examine learners knowledge organization with multiple external representations (MER) in an argumentation-based computer-supported collaborative learning environment. For this purpose, an argumentation-based socioscientific unit on nuclear energy has been developed and implemented with a group of preservice science teachers (n=20), who enrolled in a Physical Sciences for Middle School Teachers Content and Methods courses at a Southeastern public research university in the USA. During the unit, the participants used a new hypertext platform that incorporated three external representational formats. This technology enables knowledge organization, collaboration, and classroom management tools. In the unit, the students were asked to use the platform individually and learn about nuclear energy. Later in the unit, the students engaged in argumentation about the issue in their small groups and were asked to organize knowledge on a specific scientific aspect of the nuclear energy. Finally, the students presented their findings and final arguments about nuclear energy use and power plant construction to the whole class.This study documented the students knowledge organization with MER, their argumentation qualities, and the interaction between students knowledge organization and argumentation practices. The findings of the study showed that students mostly relied on their Wiki and ConceptMaps in the unit. These representation types were more centralized and had higher knowledge organization quality scores than pictorial representations created by the students. Also, two focus students argumentation practices indicated that when they were asked to present their groups argumentation based on their collaborative knowledge organization, the student with the low knowledge organization and individual argumentation score incorporated more justifications, aspects, and a counterargument in the collaborative argument she presented. The student with a high knowledge organization and argumentation score, on the other hand, used specific scientific knowledge to support her argument and maintained the high quality of argument. Finally, interaction analysis indicated that the focus groups knowledge organization practices interacted bi-directionally in this settings and students use of representations differed in small group argumentation and the class presentation. Implications for curriculum designers, science teachers, and feature research directions were discussed.