This study examined the differential impacts of an inquiry-based instruction on conceptual changes across levels of prior knowledge and reading ability. The instrument emphasized four simultaneously important components: conceptual knowledge, reading ability, attitude toward science, and learning environment. Although the learning patterns and effect size analyses indicated that students from all subgroups demonstrated substantial gains on weather concepts, students from the low prior conceptual knowledge group demonstrated greater gains in conceptual knowledge than subgroups with more prior knowledge; and these gains remained stable 3 weeks after the instruction ceased. However, students from the low language proficiency group showed the least gains in conceptual knowledge. Students' prior knowledge and reading ability were found to be positively and significantly associated to conceptual development. Recent perspectives on the role of language in science education and suggestions that support learning during instruction are briefly described.