Science notebooks can play a critical role in activity-based science learning, but the tasks of recording, organizing, analyzing, and interpreting data create barriers that impede science learning for many students. This study (a) assessed in a randomized controlled trial the potential for a web-based science notebook designed using the Universal Design for Learning (UDL) framework to overcome the challenges inherent in traditional science notebooks, (b) explored how teacher characteristics and student use of supports in the digital environment were associated with productive inquiry science learning behaviors, and (c) investigated students' and teachers' perceptions of the key affordances and challenges of the technology to their learning. Use of the UDL science notebook resulted in improved science content learning outcomes (y = .34, p < .01), as compared with traditional paper-and-pencil science notebooks, and positively impacted student performance to the same degree, regardless of reading and writing proficiency and motivation for science learning at pretest. Students of teachers with greater experience using science notebooks and students who more frequently used the contextual supports within the notebook demonstrated more positive outcomes. Students and teachers reported overall quite positive experiences with the notebook, emphasizing high levels of interest, feelings of competence, and autonomy.