PlantingScience (PS) is a unique web-based learning system designed to develop secondary students' scientific practices and proficiencies as they engage in hands-on classroom investigations while being mentored online by a scientist. Some students' teachers had the opportunity to attend PS professional development (PD). In this dissertation, I developed a process of assessing student learning outcomes associated with their use of this system and evaluated inquiry engagement within this system. First, I developed a valid and reliable instrument (Online Elements of Inquiry Checklist; OEIC) to measure participants' (students, scientists, and teachers) engagement in scientific practices and proficiencies embedded within an inquiry cycle I collaborated with an expert-group to establish the OEIC's construct and content validities. An inter-rater reliability coefficient of 0.92 was established by scientists and a split half analysis was used to determine the instruments' internal consistency (Spearman-Brown coefficient of 0.96). Next, I used the OEIC to evaluate inquiry cycle engagement by the participants who used the PS online platform designed by the Botanical Society of America which facilitated communication between participants. Students provided more evidence of engagement in the earlier phases of an inquiry cycle. Scientists showed a similar trend but emphasized experimental design and procedures. Teachers rarely engaged online. Exemplary students' outcomes followed similar inquiry cycle trends, but with more evidence of engagement with one notable difference. Exemplary students provided evidence for extensive engagement in immersion activities, implicating immersion as a crucial component of successful inquiry cycle engagement. I also compared engagement outcomes of students whose teachers attended the PD experience to the students of teachers who did not attend PD. Differences found between the two groups occurred throughout the inquiry cycle, typically associated with experiences provided during the PD. As a result of this research I have several recommendations about revisions to the PS online platform and use of approaches to assure students development of scientific practices and proficiencies. The recommendations include additional scaffolding of the platform, explicit inquiry cycle instruction, and continued opportunities for teachers to engage in PD experiences provided by PS.