Inquiry instruction often neglects graphing. It gives students few opportunities to develop the knowledge and skills necessary to take advantage of graphs, and which are called for by current science education standards. Yet, it is not well known how to support graphing skills, particularly within middle school science inquiry contexts. Using qualitative graphs is a promising, but underexplored approach. In contrast to quantitative graphs, which can lead students to focus too narrowly on the mechanics of plotting points, qualitative graphs can encourage students to relate graphical representations to their conceptual meaning. Guided by the Knowledge Integration framework, which recognizes and guides students in integrating their diverse ideas about science, we incorporated qualitative graphing activities into a seventh grade web‐based inquiry unit about cell division and cancer treatment. In Study 1, we characterized the kinds of graphs students generated in terms of their integration of graphical and scientific knowledge. We also found that students (n = 30) using the unit made significant learning gains based on their pretest to post‐test scores. In Study 2, we compared students' performance in two versions of the same unit: One that had students construct, and second that had them critique qualitative graphs. Results showed that both activities had distinct benefits, and improved students' (n = 117) integrated understanding of graphs and science. Specifically, critiquing graphs helped students improve their scientific explanations within the unit, while constructing graphs led students to link key science ideas within both their in‐unit and post‐unit explanations. We discuss the relative affordances and constraints of critique and construction activities, and observe students' common misunderstandings of graphs. In all, this study offers a critical exploration of how to design instruction that simultaneously supports students' science and graph understanding within complex inquiry contexts.