The study investigated if young students internalized content and concepts embedded in a science computer microworld simulation as opposed to treating it as merely a game to be played. The article reports changes in the Grade Two students' cognitive outcomes and processes after learning with the software integrated within a thematic curriculum in a classroom over a period of six weeks. Results indicate improvement in various thinking skills and strategies, from basic recall to the higher level skills such as classification and inference, as well as in the children's usage of scientific language. Transfer occurred but was not significant thereby emphasizing the importance of providing numerous practices instead of relying on the software to teach higher order cognitive skills. Daily usage and a flexible paired working environment with the computer were pedagogical variables in the cognitive outcomes.