Although extensive research has shown the important educational value of technology-enhanced online units on students' science learning, few studies have looked at upper elementary students' knowledge integration in a web-based inquiry science environment (WISE). This case study investigates how upper-elementary students responded to an online prompt, in an embedded assessment tool, to construct a scientific explanation around the variation of traits in their class and how a teacher provided feedback to encourage student discourse. Our findings show that students were able to identify which traits were more common in their class; however, they struggled with making a connection between variation of traits and inheritance of traits when analyzing data from their pie chart. Additionally, we show that an upper-elementary teacher used an embedded assessment tool to scaffold the iterative process of learning and feedback that occurs in an online platform that leverages learning technologies by engaging in high-level discourse moves. We suggest that teachers' use of embedded assessments in a technology-enhanced environment can encourage student self-reflection and support teachers in making evidence-based instructional decisions as well as provide immediate feedback along the way, which is a key support when students are not participating in traditional face-to-face classroom environments.