In recent years, there has been a strong push to transform STEM education at K-12 and collegiate levels to help students learn to think like scientists. One aspect of this transformation involves redesigning instruction and curricula around fundamental scientific ideas that serve as conceptual scaffolds students can use to build cohesive knowledge structures. In this study, we investigated how students use mass balance reasoning as a conceptual scaffold to gain a deeper understanding of how matter moves through biological systems. Our aim was to lay the groundwork for a mass balance learning progression in physiology. We drew on a general models framework from biology and a covariational reasoning framework from math education to interpret students' mass balance ideas. We used a constant comparative method to identify students' reasoning patterns from 73 interviews conducted with undergraduate biology students. We helped validate the reasoning patterns identified with >8000 written responses collected from students at multiple institutions. From our analyses, we identified two related progress variables that describe key elements of students' performances: the first describes how students identify and use matter flows in biology phenomena; the second characterizes how students use net rate-of-change to predict how matter accumulates in, or disperses from, a compartment. We also present a case study of how we used our emerging mass balance learning progression to inform instructional practices to support students' mass balance reasoning. Our progress variables describe one way students engage in three dimensional learning by showing how student performances associated with the practice of mathematical thinking reveal their understanding of the core concept of matter flows as governed by the crosscutting concept of matter conservation. Though our work is situated in physiology, it extends previous work in climate change education and is applicable to other scientific fields, such as physics, engineering, and geochemistry.