Diverse implicit cognitive elements seem to support but also constrain reasoning in different domains. Many of these cognitive constraints can be thought of as either implicit assumptions about the nature of things or reasoning heuristics for decision-making. In this study we applied this framework to investigate college students' understanding of structure-property relationships in the context of chemical reactivity. The ability to understand and apply structure-property relationships to explain the behavior of physical, chemical, and biological systems is a core competence that many science and engineering majors are expected to develop. Core findings were derived from semi-structured interviews based on a ranking task. Study participants relied on intuitive, spurious, and valid assumptions about the nature of chemical entities in building their responses. In particular, many of students appeared to conceive chemical reactions as macroscopic reassembling processes thought to be more favored the easier it seemed to break reactants apart or put products together. Students also expressed spurious chemical assumptions based on the misinterpretation and overgeneralization of chemical ideas. Reasoning heuristics for decision-making also played a significant role in the construction of answers to ranking questions. Specifically, interviewees demonstrated strong over-reliance on variable reduction strategies and recognition memory in their reasoning. Our findings reveal the need for educational approaches that more effectively affect the conceptual sophistication and depth of reasoning about structure-property relationships of college students. Our research framework provides a productive approach for the analysis of student reasoning in scientific domains. (Contains 3 tables.)