Manipulative environments play a fundamental role in inquiry-based science learning, yet how they impact learning is not fully understood. In a series of two studies, we develop the argument that manipulative environments (MEs) influence the kind of inquiry behaviors students engage in, and that this influence realizes through the affordances of MEs, independent of whether they are physical or virtual. In particular, we examine how MEs shape college students' experimentation strategies and conceptual understanding. In study 1, students engaged in two consecutive inquiry tasks, first on mass and spring systems and then on electric circuits. They either used virtual or physical MEs. We found that the use of experimentation strategies was strongly related to conceptual understanding across tasks, but that students engaged differently in those strategies depending on what ME they used. More students engaged in productive strategies using the virtual ME for electric circuits, and vice versa using the physical ME for mass and spring systems. In study 2, we isolated the affordance of measurement uncertainty by comparing two versions of the same virtual ME for electric circuits--one with and one without noise--and found that the conditions differed in terms of productive experimentation strategies. These findings indicate that measures of inquiry processes may resolve apparent ambiguities and inconsistencies between studies on MEs that are based on learning outcomes alone.