This study was conducted to determine the differences in the conceptual understanding of 52 Turkish students who were taught with a scientific argumentation approach in grade 12 chemistry. The concept test was administered to the participants as a pre-test and post-test, and it contained two questions. The first had two sub-questions had two steps. The second had six sub-questions. The researcher of the current study, who was well-versed in chemistry education, and a chemistry teacher, expressed their views regarding the content validity of the concept test. The criteria scales and scoring rubrics were prepared by the researcher to evaluate the test in terms of a conceptual understanding of hydrogen bonding. This study, which thoroughly aims at learning the effects of scaffolding with argumentation, applied mixed-methods research to reveal students' understanding of hydrogen forces and to determine schemas by drawing. In quantitative analysis, the mean, median, and standard deviation values of the data collected from the students were considered. In qualitative analysis, the drawings and explanations of the students on the concept tests applied before and after the education were discussed. According to the results of the concept tests, improvement in the conceptual understanding of the students before and after the argumentation-based teaching could be observed; however, half of the students still evidently had a rote understanding. In conclusion, the scientific-argumentation-based teaching approach was effective in developing their conceptual understanding. Recommendations are made as a result of this study.