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Computational modeling of scientific systems is a powerful approach for fostering science and computational thinking (CT) proficiencies. However, the role of programming activities for this synergistic learning remains unclear. This paper examines alternative ways to engage with computational models (CM) beyond programming. Students participated in an integrated Science, Engineering, and Computational Modeling unit through one of three distinct instructional versions: Construct a CM, Interpret-and-Evaluate a CM, and Explore-and-Evaluate a simulation. Analyzing 188 student responses to a science+CT embedded assessment task, we investigate how science proficiency and instructional versions related to pseudocode interpretation and debugging performances. We found that students in the Explore-and-Evaluate a simulation outperformed students in the programming-based versions on the CT assessment items. Additionally, science proficiency strongly predicted students’ CT performance, unlike prior programming experience. These results highlight the promise of diverse approaches for fostering CT practices with implications for STEM+C instruction and assessment design.