Course-based undergraduate research experiences (CUREs) are being championed as scalable ways of involving undergraduates in science research. Studies of CUREs have shown that participating students achieve many of the same outcomes as students who complete research internships. However, CUREs vary widely in their design and implementation, and aspects of CUREs that are necessary and sufficient to achieve desired student outcomes have not been elucidated. To guide future research aimed at understanding the causal mechanisms underlying CURE efficacy, we used a systems approach to generate pathway models representing hypotheses of how CURE outcomes are achieved. We started by reviewing studies of CUREs and research internships to generate a comprehensive set of outcomes of research experiences, determining the level of evidence supporting each outcome. We then used this body of research and drew from learning theory to hypothesize connections between what students do during CUREs and the outcomes that have the best empirical support. We offer these models as hypotheses for the CURE community to test, revise, elaborate, or refute. We also cite instruments that are ready to use in CURE assessment and note gaps for which instruments need to be developed.