Water sciences education is paramount to sustainable groundwater resource management, especially of drinking water, but misunderstandings about groundwater among non-experts remain widespread. Groundwater residence is an especially challenging concept to learn because it is not directly visible in typical circumstances. The present study uses a quasi-experimental research design to compare the impacts that two instructional sequences have on improving students' conceptual understanding of groundwater residence and aquifers. Both instructional sequences are designed to use active learning, but only one solicits and engages students' preconceptions. The theoretical framework for this study is the knowledge integration perspective of conceptual change. As such, this study considers cognitive, temporal, and social dimensions of learning. To assess students' learning, concept sketches were analyzed using diagrammatic and textual content analyses, normalized learning gains were calculated, multiple-choice items were scored dichotomously (i.e., scored as either correct or incorrect), free-response items were scored for partial credit, and classroom observations tracked social interactions. We found significantly larger learning gains when students' preconceptions were explicitly incorporated into the instructional sequence compared to when they were not taken into account. We also found the prior-knowledge instructional sequence (PKIS) positively impacted both Caucasian and non-Caucasian students as well as male and female students. Our findings indicate that actively engaging students' prior knowledge in the ways that were researched herein can be a high impact teaching practice and is worthy of future research in other specific domains beyond groundwater residence and aquifers.