This study examined 6th graders’ use of the VoiceThread app as part of a science inquiry project on photosynthesis and carbon dioxide emissions in terms of their ability to engage in causal reasoning and their use of the affordances of multimodality, collaboration, interactivity, and connectivity. Students employed multimodal production using images with audio or written annotations on VoiceThread to describe their analysis of the photosynthesis process. Analysis of these annotations indicated that the majority of those annotations represented causal reasoning reflecting the use of science inquiry thinking. Students reported that working collaboratively in pairs mediated by a shared focus on the same images and formulation of annotations enhanced sharing of alternative perspectives. Being able to readily share their VoiceThread productions with peers and the teacher enhanced their sense of purpose and audience driving their work. And making intertextual connections between alternative meanings of images led students to critically analyze these images. This study suggests how these affordances are mediated through use of VoiceThread to engage students in science inquiry.