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During processing, visualization and analysis of multi-variable oceanographic data sets from an AUV it can be challenging to both maintain overview and pay attention to detail. We here describe a software system intended to bridge this gap and discuss its application on ADCP and CTD data recently acquired by the HUGIN 1000 AUV in the Barents Sea. The software, ANCOR II, features interactive graphics functionality designed to facilitate comprehension of the relationship between spatial/temporal characteristics of the surveyed environment, the sampling process and the sampled data. It Earth-references the sensor data by means of vehicle navigation data and offers temporal/spatial averaging and various visualization options for the processed results. The user navigates the temporal and spatial distribution of vector and scalar data through interconnected plots of vehicle trajectory, current velocity profiles and time-series. The system differs from vessel-mounted ADCP software solutions by handling data from ADCPs that have been moving in three dimensions as well as concurrently sampled CTD data from the same platform. The main objective of the described case-study survey was to investigate the spatio-temporal distribution of diapausing zooplankton organisms. The AUV sensor package comprised an ADCP, a CTD and an LOPC. The paper discusses how the software facilitates processing of AUV-ADCP-CTD data and helps visualizing the data to ease the interpretation of dominant features.