The paper traces a research process in the design and development of a science learning environment called WiMVT (web-based inquirer with modeling and visualization technology). The WiMVT system is designed to help secondary school students build a sophisticated understanding of scientific conceptions, and the science inquiry process, as well as develop critical learning skills through model-based collaborative inquiry approach. It is intended to support collaborative inquiry, real-time social interaction, progressive modeling, and to provide multiple sources of scaffolding for students. We first discuss the theoretical underpinnings for synthesizing the WiMVT design framework, introduce the components and features of the system, and describe the proposed work flow of WiMVT instruction. We also elucidate our research approach that supports the development of the system. Finally, the findings of a pilot study are briefly presented to demonstrate of the potential for learning efficacy of the WiMVT implementation in science learning. Implications are drawn on how to improve the existing system, refine teaching strategies and provide feedback to researchers, designers and teachers. This pilot study informs designers like us on how to narrow the gap between the learning environment's intended design and its actual usage in the classroom.