This paper examines how practicing teachers approach and evaluate students' critical thinking processes in science, using the implementation of an online, inquiry-based investigation in middle school classrooms as the context for teachers' observations. Feedback and ratings from three samples of science teachers were analysed to determine how they valued and evaluated component processes of students' critical thinking and how such processes were related to their instructional approaches and student outcomes. Drawing from an integrated view of teacher practice, results suggested that practicing science teachers readily observed and valued critical thinking processes that aligned to goal intentions focused on domain content and successful student thinking. These processes often manifested as components of effective scientific reasoning--for example, gathering evidence, analysing data, evaluating ideas, and developing strong arguments. However, teachers also expressed avoidance intentions related to student confusion and uncertainty before and after inquiry-based investigations designed for critical thinking. These findings highlight a potential disconnect between the benefits of productive student struggle for critical thinking as endorsed in the research on learning and science education and the meaning that teachers ascribe to such struggle as they seek to align their instructional practices to classroom challenges.