This research explored kindergarten students' learning of simple particle models to explain the properties and behavior of matter in the solid, liquid, and gas states and during phase transitions (evaporation, melting, freezing, and condensation). Science instruction for young learners tends to focus on the concrete and directly observable. This focus on the here and now of experience can foreclose opportunities for young learners to explain their world in terms of the mechanisms posited by modern science. The current research examined how kindergarten children's models of matter develop as they engage with technology-mediated, model-based inquiry lessons. Data were collected from two intervention groups who engaged in a series of modeling lessons with the aid of digital tools for visualizing and explaining particle behavior across varied material phenomena. The two intervention groups engaged in a common set of modeling activities but differed in the use of one digital tool. Intervention students were interviewed in the week before the beginning of the intervention and the week following the completion of the intervention to assess the development of their models of matter. To provide a baseline for comparison, we assessed a third group of kindergarten children who did not receive any instruction on matter in the same time frame as the intervention students. Data were coded using cognitive science techniques of verbal protocol analysis. Repeated measures ANOVAs were conducted to explore changes across the pre- and post-intervention interviews. We found that children from both intervention groups showed significant gains in the use of particle models to explain material phenomena, while the comparison group showed only small gains in the use of particle models.