The Indiana Science Initiative (ISI) is a systemic effort to reform K-8 science education. The program provides teachers with professional development, reform-oriented science modules, and materials support. To examine the impact of the initiative's professional development, a participant observation study was conducted in the program's pilot year. Five teachers in grades 3-6 were observed and interviewed as they implemented the ISI-provided modules. Analysis of the observation data revealed that the teachers incorporated each of the features of inquiry science instruction. However, they did not consistently teach in a way that was aligned with the intent of the ISI. Examination of interview data provided insight into influences on teachers' use of inquiry with the ISI-provided modules. These data revealed that teachers were aware of the intent of the ISI and attempted to align their instruction. However, teachers were influenced by their perceptions of students' behavior and abilities as well as timing and the appropriate level of teacher control needed to facilitate science instruction. The research suggests that professional development activities should prepare teachers to help learners evaluate explanations against alternatives, connect explanations to scientific knowledge, and provide strategies to address teachers' perceptions of students, timing, and teacher control.