Improving Instruction in Groundwater Numerical Modeling Using Inquiry-Based Learning: Insights from a Grid Construction Case Study

(1) Background: Groundwater numerical modeling education often suffers from passive student imitation, which limits the development of higher-order thinking and knowledge internalization. To address this challenge and promote a shift in instructional philosophy, inquiry-based learning (IBL) was implemented. However, the mechanisms underlying its effectiveness require further elucidation to guide this transformation. (2) Methods: This study was conducted with a cohort of 63 third-year environmental engineering students. It compares the outcomes of the IBL approach, focused on the geometric requirements of grid construction for the control-volume finite-difference (CVFD) method, against those of traditional instruction. (3) Results: The findings demonstrate that IBL’s effectiveness is strongly moderated by students’ prior knowledge. Learners with stronger prior knowledge exhibited a 330% increase in higher-order thinking (p = 0.04), reflected in a shift toward complex, terrain-adapted Voronoi grids. However, their understanding of core CVFD geometric concepts only improved moderately (34%), reflecting the nonlinear and by-product nature of knowledge acquisition in inquiry-based pathways. In contrast, students with weaker prior knowledge devoted most of their cognitive resources to basic concept understanding, and their limited cognitive schemas constrained their ability to process new information. Therefore, no measurable improvement was observed in either higher-order thinking or conceptual mastery in this group. (4) Conclusions: The key innovation of this study lies in revealing prior knowledge as a critical moderator, highlighting how the effectiveness of IBL depends on its interaction with the learner’s individual characteristics. This mechanistic insight provides a cognitive framework for differentiated instructional design in engineering education, ensuring that pedagogical advancements translate into equitable learning gains.