In this mixed-method study, we investigated whether the use of a web-based inquiry science environment (WISE) unit would improve the knowledge integration (KI) of middle school students with no formal school-based prior experience with inquiry instruction. A unit on heat and temperature that reflected KI principles and processes was designed and developed using the WISE legacy-authoring tool. A KI Instrument for heat and temperature was developed and used to evaluate students' KI levels. The WISE logs of three students with different KI improvement levels were analyzed qualitatively to identify the more critical KI processes that could explain different levels of KI improvement. The results showed that students improved their KI levels significantly after participating in the WISE-based unit. The findings highlighted the need to provide better scaffolding and support for two of the KI instructional processes in particular: distinguishing among ideas and sorting out ideas--especially in settings where students have no formal school-based prior inquiry experience in science classes.