Over the last 30 years there has been a wide-spread implementation of inquiry based classes in science education (1), and in tertiary physiology curricula in particular (2), because these pedagogies have been shown to improve student learning of content (3, 4) and important scientific thinking skills such as experimental design and data interpretation (5). However, a multitude of obstacles face instructors aiming to implement inquiry-based practical curricula (6) where poor implementation (7), and both too much and too little guidance (8) have negative effects on student learning. It is therefore important to understand which specific aspects of inquiry-based curricula engage students in effectively developing scientific thinking skills, and when and why the development of these skills goes awry. We have developed a vertically-integrated set of inquiry-based practical curricula for large cohorts (500-900 students) of first and second year physiology students (9) which facilitate the development of students’ skills in scientific thinking (10, 11). Video recordings of students engaged in inquiry in class were analysed using the Australian national academic standards for scientific thinking (12) and the theoretical framework for critical thinking developed by Bailin (13). Results from this study showed that students used and developed their critical scientific thinking skills when they needed to make scientific decisions. In our physiology practical classes, these decisions typically involved which hypothesis to test and how, and how to analyse and interpret experimental data. Students employed a range of strategies to make these decisions, from uncritical guesses, to using their prior anecdotal experience and instructions from manuals or teaching assistants, through to more scientifically rigorous strategies that included using evidence from their own experiments and scientific literature. Evidence from video tapes of classes has revealed key factors that impact on the degree of scientific rigour students employ when making their decisions. For example, students must be required to 1) demonstrate feasibility of their experimental proposals with pilot data and primary literature, and 2) to critically compare experimental contexts and specific data values when interpreting their experimental findings. This study provides evidence-based strategies for producing curricula that are effective in helping large cohorts of early stage undergraduate physiology students to develop advanced scientific thinking skills.