In South Africa, there is a strong curriculum imperative for South African school science teachers to not only involve learners in practical inquiry activities but also to support students in making a connection between the construction of substantive scientific knowledge to these activities. The research reported in this article investigated the extent to which South African teachers at historically disadvantaged township schools engaged students in the construction of science ideas in inquiry lessons. To this end, video transcripts of thirty two lessons were analysed and coded using a framework of student thinking lens developed by the Biological Sciences Curriculum Study (BSCS) for the Science Teachers Learning from Lesson Analysis (STeLLA) project. The trends on the teaching features are explicated in the presentation of an in-depth analysis of a chemistry lesson. This research suggests the need for a re-alignment of inquiry-based science education with the development of science ideas.