The purpose of this quasi-experimental study was to explore how seventh graders in a suburban school in the United States developed argumentation skills and science knowledge in a project-based learning environment that incorporated a graph-oriented, computer-assisted application. A total of 54 students (three classes) comprised this treatment condition and were engaged in a project-based learning environment that incorporated a graph-oriented, computer-assisted application, whereas a total of 57 students (three classes) comprised the control condition and were engaged in a project-based learning environment without this graph-oriented, computer-assisted application. Verbal collaborative argumentation was recorded and the students' post essays were collected. A random effects analysis of variance (ANOVA) was conducted and a significant difference in science knowledge about alternative energies between conditions was observed. A multivariate analysis of variance (MANOVA) was conducted and there was a significant difference in counterargument and rebuttal skills between conditions. A qualitative analysis was conducted to examine how the graph-oriented, computer-assisted application supported students' development of argumentation skills and affected the quality of collaborative argumentation. The difference in argumentation structure and quality of argumentation between conditions might explain a difference in science knowledge as well counterargument and rebuttal skills (argumentation) between both conditions. This study concluded that a project-based learning environment incorporating a graph-oriented, computer-assisted application was effective in improving students' science knowledge and developing their scientific argumentation skills.