This study implements a design-based research approach to design and evaluate different scaffolding strategies for supporting student learning as well as promoting student agency within a computational science course. The course introduces computational methods and tools in the context of disciplinary problems for materials science and engineering students. Initial course offerings suggested that students were overwhelmed by the interdisciplinary nature of the course. Therefore, the research team evaluated different scaffolding strategies for supporting students' learning, and how those may have provided students with agency to self-scaffold when needed. Three rounds of data collection included 17 students who participated in individual semi-structured interviews to explore how they used (or not) different scaffolds. Five of the participants were recruited for the first iteration; six of them were recruited in the second iteration, and six more in the third one. The iterative process allowed us to adapt the scaffolding procedures for the third iteration from the data collected in iterations 1 and 2. The purpose of this study is to understand how students used different scaffolds, and what implementation strategies were effective according to student uses of these scaffolds in the context of computational science. The results suggest that students developed agency to self-scaffold when needed, as they benefited from multiple scaffolds at different steps of the problem-solving process. Moreover, providing worked examples without engaging students in their active exploration can be ineffective, but this engagement can be achieved using written explanations. Additional support may be needed at an early stage of skill development, so students have an idea of how to validate their model.