Constructivist learning theories consider deep understanding of the content to be the result of engagement in relevant learning activities with appropriate scaffolding that provides the learner with timely and substantive feedback. However, any group of students has a variety of levels of knowledge and cognitive development, which makes providing appropriate individual-level scaffolding and feedback challenging in the classroom. Computer simulations can help meet this challenge by providing technology-enhanced embedded scaffolding and feedback via specific simulation design. The use of computer simulations does not, however, guarantee development of deep science understanding. Careful research-driven design of the simulation and the accompanying teaching structure both play critical roles in achieving the desired learning outcomes. In this paper, we discuss the capabilities of computer simulations and the issues that can impact the learning outcomes when combining technology-enhanced scaffolding and feedback with external teaching structures. We conclude with suggestions of promising research avenues on simulation design and their use in the classroom to help students achieve deep science understanding.