This paper discusses the results of two experiments assessing undergraduate students' beliefs about the random nature of molecular environments. Experiment 1 involved the implementation of a pilot adaptive assessment (n = 773) and focus group discussions with undergraduate students enrolled in first- through third-year biology courses; experiment 2 involved the distribution of the redesigned adaptive assessment to the same population of students in three consecutive years (n = 1170). The overarching goal of the study was to provide a detailed characterization of learners' perceptions and beliefs regarding molecular agency, environments, and diffusion and whether or not those beliefs change over time. Our results indicated that advanced learners hold as many misconceptions as novice learners and that confidence in their misconceptions increases as they advance through their undergraduate education. In particular, students' understanding of random/ Brownian motion is complex and highly contextual, suggesting that the way in which we teach biology does not adequately remediate students' preconceived notions of molecular agency and may actually reinforce them.