Ensuring that all students, including English language learners (ELLs) who speak English as a second language, succeed in science is more challenging with a shift towards learning through language-intensive science practices suggested by the Next Generation Science Standards (NGSS). Interactive visualization technologies have the potential to support science learning for all students, including ELLs, by providing explicit representations of unobservable scientific systems. However, whether and how such technologies can be beneficial for these underserved students has not been sufficiently investigated. In this study, we examine the short-term and long-term effects of interactive visualizations in improving linguistically diverse eighth-grade students' understanding of properties of matter and chemical reactions during inquiry instruction. The results show that after interacting with the visualizations, both ELLs and non-ELLs showed significant improvement in their understanding of the target concepts at the molecular level on both the immediate test and the delayed test (3 months after the study). In particular, aligned with the goals of the NGSS, all students, including ELLs, were able to demonstrate their understanding of how energy and matter are involved in chemistry through developing molecular models, critiquing models, and constructing scientific explanations. This study shows the potential benefits of using interactive visualizations during inquiry instruction as a resource to help all students, including ELLs who are traditionally underserved in mainstream classrooms, develop a more coherent understanding of abstract concepts of molecular processes during chemical phenomena.