A learning experience designed for the Next Generation Science Standards (NGSS) should integrate the Science & Engineering Practices and Crosscutting Concepts (CCCs) with science content. Such "three-dimensional learning" engages students in the epistemic components of the scientific process. Whether the Practices and CCCs are used in epistemically meaningful ways to build more expert-like understanding and behaviors is context dependent. The NGSS defines learning progressions for the Practices and CCCs, but they do not provide the detail needed to build activities within the grade bands. It is also up to curriculum developers to decide how to incorporate the Practices and CCCs using technology in domain-specific inquiry contexts. We document the development and evaluation of the week-long middle school summer Camp NANO, where campers participated in an observational investigation of a stream habitat from the macro-to-nano scale using the scanning electron microscope (SEM) as well as produced an interactive Virtual Field Environment (VFE) communication of the stream environment. This pilot is an example of a domain-specific authentic scientific inquiry experience built around three-dimensional learning as guided by the novice-to-expert literature to meet the NGSS middle school learning targets of the selected Practices and CCCs. We found that it was possible to build an activity plan that authentically incorporated and integrated the Practices and CCCs with the SEM and VFE, and that the involvement with the SEM and VFE in association with the observational investigation facilitated expert-like thinking and behaviors towards the selected Practices and CCCs.