Inquiry activities with component visualization tools are increasingly prevalent in K-12 STEM classrooms; however, evidence of their efficacy has primarily been collected from controlled laboratory studies that lack ecological validity or from small-scale classroom interventions that assess learning outcomes proximal to the intervention. Here, the long-term, differential impact of visualization-supported inquiry activities on learning outcomes was examined in the context of secondary chemistry. Student learning was assessed on summative content assessments completed by a cohort of 1152 students who used visualization-supported inquiry activities from "The Connected Chemistry Curriculum" during a school year. Results demonstrate that the cohort performed significantly better on ACS Conceptual Exam assessment items aligned with curriculum learning objectives. This study demonstrates that visualization tools embedded in inquiry activities result not only in short-term gains but in long-term improvements relative to business-as-usual practices.