In this study, we discuss the scaffolded design of ODRES (Observe, Discuss, and Reason with Evidence in Science), a computer tool that was designed to be used with elementary school children in science, and report on the effects of learning with ODRES on students' conceptual understandings about light, color, and vision. Succinctly, dyads of sixth-grade students were engaged in distributed collaborative inquiry regarding the scientific concepts of light, vision, and color in order to solve a mystery problem about a stolen diamond. ODRES was employed to scaffold students' collaborative inquiry with different tools, such as the simulator that simulates the effects of the color of a light source on an object, the magnifying glass that enables students to make careful observations, and the notebook that organizes the results of students' investigations. Students performed two cycles of collaborative inquiry, and each cycle was followed by a classroom discussion where students could present their solutions, share information, reflect, raise questions, and get feedback about their proposed solutions. The results showed that learning with ODRES positively affected students' understandings and promoted a lasting effect on their conceptions. Moreover, the results provide useful guidance about how ODRES can be used as a learning tool in collaborative inquiry, and explain the role of discussion and investigation of inquiry processes at the level of a distributed cognitive system. Implications for designing distributed educational systems for children are finally discussed. (Contains 5 figures and 3 tables.)