Drawing, constructing, and explaining a model of a given abstract phenomenon is a challenging task. In this study, students were engaged in the "Project-Based Inquiry Science (PBIS)-Air Quality" learning unit, as part of their chemistry curriculum. The study aim is to determine how well students understand chemistry conceptually after completing the PBIS Air-Quality learning unit. Using their pre- and post-closed-ended questions as well as their post-drawing assignment, we developed a rubric to examine students' conceptual understanding as manifested in their drawings and examined if there is a correlation between their drawings and their pre- and post-questionnaire results. Research participants were 436 eighth-grade middle school students. The results suggest that state of matter and distance between molecules were conceptually understood better after learning the PBIS unit. We analyzed students' explanations and drawings based on the rubric and found a moderate positive correlation between students' post-scores in the questionnaires and their answer complexity level in the post drawing assignment. The research shows that students' conceptual understanding should be assessed through different assessment methods to gain a better evaluation of students' conceptual understanding. Even students who succeeded in the close-ended questions in the post-questionnaire had difficulties expressing their conceptual understanding through the drawing assignment. The rubric can help teachers and educators assess their students' conceptual models and can be used as an assessment tool to evaluate the progression of their chemistry understanding. Teaching with rubrics will improve the quality of assessment and facilitate teachers' development.