This classroom study examined the role of low-achieving students' self-regulated learning (SRL) behaviors and their teacher's scaffolding of SRL while using a Web-based water quality simulation environment to learn about ecological systems. Forty-nine 11th and 12th grade students learned about ecology and the effects of land use on water quality by collaboratively using the RiverWeb SM water quality simulation (WQS) during a two-week curriculum on environmental science. The students' emerging understanding was assessed using pretest and posttest scores. Students' self-regulatory behaviors and teacher's scaffolding of SRL were assessed through an analysis of their discourse during several collaborative problem-solving episodes. Findings indicate that students learned significantly more about ecology after working collaboratively with the WQS. However, these learning gains were quite small and were related to the self-regulatory behaviors observed in the dyads and their teacher's scaffolding and instruction. Analyses of video data indicate that a large amount of time was spent by the dyads and teacher in using only a few strategies, while very little time was spent on planning, monitoring, and handling task difficulties and demands. Further analysis revealed that both the dyads and teacher were using low-level strategies (e.g., following procedural tasks, evaluating the content, searching, and selecting informational sources in the WQS) to learn about the topic. Our results provide a valuable initial characterization of the complexity of self-and other-regulated learning in a complex, dynamic, technology-enhanced, student-centered science classroom. We discuss how the results will be used to inform the design of computers as MetaCognitive tools designed to foster students' learning of conceptually challenging science topics.