Physics education research over the past few decades has made significant advances toward improving instructional practices and developing effective instructional materials for physics classrooms. In some contexts, however, after multiple instructional refinements difficulties can remain persistent. Recent findings in PER suggest that many of these difficulties are consistent with reasoning paths accounted for by dual process theories of reasoning. Students often appear to be able to employ correct conceptual understanding in one context, but neglect to demonstrate the same understanding in another closely related context. This thesis explores the use of dual-process theories of reasoning as a lens for interpreting observed patterns of student reasoning. First, we examined both the impact of problem design and the impact of instruction targeting accessible intuitive ideas in the context of sinking and floating. We found that targeted instruction which directly addressed everyday experiences had a significant impact on student performance in that context. We also found that changes to problem design and instruction emphasizing correct approaches had little impact on performance. Further investigations into the cognitive mechanisms behind student reasoning patterns found a positive relationship between student cognitive reflection skills and performance on Newton's third law problems. Findings suggest that those with higher cognitive reflection skills, as measured by the CRT, are more likely to 1) answer correctly on problems which elicit intuitively appealing but incorrect answers 2) provide correct and complete physical justification to problem solutions and 3) answer problems consistently. Finally, we examined student reasoning patterns in the context of mechanical waves. We attempted to influence intuitive approaches with video simulations of the physical situation. We found that students tended to reason with mathematical approaches and had difficulty overcoming intuitive ideas even after viewing the physical simulation.