Depression is one of the top mental health concerns among undergraduates and disproportionately affects students who are underrepresented in science. As such, understanding how emerging science learning environments, such as online science courses, affect students with depression is integral to creating a more inclusive scientific community. In this exploratory study, we interviewed 24 undergraduates with depression who were pursuing an online BS degree in biological sciences at a research-intensive institution. We assessed how students perceived depression affected their learning, and in turn, how online science courses affected their depression. Using a hybrid approach of deductive and inductive coding, we found that students reported depression negatively affected an array of cognitive domains when learning science online, including students' effort, focus, and time management. Students reported that the fast pace of online courses, the lack of needing to show up to a class in person, and difficulty developing relationships with other students commonly exacerbated their depression. Conversely, the flexibility of completing course work when and where students wanted, developing a relationship with the instructor, and the ease of having questions answered online positively affected students' depression. This study provides insight into ways to create inclusive online learning environments for students with depression.