Advances in graphing technologies and learning sciences pedagogy have the potential to equitably support students when exploring complex systems depicting dynamic relationships across multiple disciplinary topics in Science, Technology, Engineering, and Mathematics (STEM). We report on the cumulative impact of science units designed in a Research Practice Partnership (RPP) that leveraged Knowledge Integration (KI) pedagogy to support middle school students to generalize insights to new graph representations and science topics. Teachers across 11 schools incorporated the graph-science units into their curriculum plans. We analyzed [approximately] 8000 responses to validated and reliable graph-science KI assessment items administered before the first year and after one, two, or three years of instruction aligned with KI pedagogy. With random coefficient, multi-level, mixed-effect regression modeling, we analyzed performance after one-, two-, and three-years of graph-science KI instruction. We also analyzed the growth trajectories of subgroups, i.e., multilingual learners. Data suggest two years of graph-science KI instruction is needed to make significant impacts on student learning and ameliorated the disparity between students with different native language fluencies. These results illustrate the value of technology-enhanced, pedagogically aligned K-12 science instruction that is designed to support connecting diverse graph data and science knowledge comprehensively and cumulatively.