This article examines the pedagogical practices of two science inquiry teachers and their students using a Web-based system called Web of Inquiry (WOI). There is a need to build a collective repertoire of pedagogical practices that can assist elementary and middle school teachers as they support students to develop a complex model of inquiry based on testing alternative hypotheses. A repertoire of effective instructional practices may help students learn the language of science, develop an understanding of scientific tools and representations, and take up a scientific worldview that emphasizes the generative, social nature of science (National Research Council [NRC], 2007). The Web of Inquiry (WOI) (http://www.webofinquiry.org) is a dynamic website where students carry out scientific inquiry projects to develop and test their theories; learn scientific language, tools, and practices of investigation; engage in self assessment; and provide feedback to peers. Two teachers and their classes participated in this study using a variety of science content. We examine and discuss the teachers' use of instructional strategies to support students to develop a coherent and theoretically driven model of scientific inquiry using the WOI. Implications of this work are addressed with respect to student and teacher learning and preservice teacher education. (Contains 2 tables, 2 figures, and 6 footnotes.)