This paper demonstrates the potential of employment of small Unmanned Aircraft Systems (mUAS) for environmental research applications and the research of natural waterway systems in particular. Specifically, we describe the recent advances in the field of navigation technologies, and methodologies for high-precision determination of position and orientation of micro aerial vehicles (MAVs), which weight does not exceed 5 kg. Although the MAV systems feature high flexibility and capability of flying into areas that are inhospitable or inaccessible to humans, the lack of precision in positioning and attitude estimation on-board decreases the gained value of the captured imagery. This limits their mode of operation to indirect georeferencing. We present a development of MAVs which can overcome such limitations due to the incorporation of a surveying grade GNSS receiver and an in-house developed Redundant Inertial Measurement Unit (R-IMU). In particular, we focus on physical integration, synchronization and quality evaluation of navigation components. After calibrating the data acquisition system, we present preliminary results from a real mapping flight.