This dissertation describes an investigation of four students' ways of thinking about functions of two variables and rate of change of those two-variable functions. Most secondary, introductory algebra, pre-calculus, and first and second semester calculus courses do not require students to think about functions of more than one variable. Yet vector calculus, calculus on manifolds, linear algebra, and differential equations all rest upon the idea of functions of two (or more) variables. This dissertation contributes to understanding productive ways of thinking that can support students in thinking about functions of two or more variables as they describe complex systems with multiple variables interacting. This dissertation focuses on modeling the way of thinking of four students who participated in a specific instructional sequence designed to explore the limits of their ways of thinking and in turn, develop a robust model that could explain, describe, and predict students' actions relative to specific tasks. The data was collected using a teaching experiment methodology, and the tasks within the teaching experiment leveraged quantitative reasoning and covariation as foundations of students developing a coherent understanding of two-variable functions and their rates of change. The findings of this study indicated that I could characterize students' ways of thinking about two-variable functions by focusing on their use of novice and/or expert shape thinking, and the students' ways of thinking about rate of change by focusing on their quantitative reasoning. The findings suggested that quantitative and covariational reasoning were foundational to a student's ability to generalize their understanding of a single-variable function to two or more variables, and their conception of rate of change to rate of change at a point in space. These results created a need to better understand how experts in the field, such as mathematicians and mathematics educators, thinking about multivariable functions and their rates of change.