The present article discusses the design and impact of computer-based visualization tools for supporting student learning and representational competence in science. Specifically, learning outcomes and student representation use are compared between eight secondary classrooms utilizing The Connected Chemistry Curriculum and eight secondary chemistry using lecture-based methods. Results from the quasi-experimental intervention indicate that the curriculum and accompanying visualization tool yield only small to modest gains in student achievement on summative assessments. Analysis of student representation use on pre- and post-assessments, however, indicate the students in Connected Chemistry classrooms are significantly more likely to use submicroscopic representations of chemical systems that are consistent with teacher and expert representation use. The affordances of visualization tools in inquiry activities to improve students' representational competence and conceptual understanding of content in the science classroom are discussed. (Contains 4 figures and 6 tables.)