This paper describes the concept, the technical implementation and the practical application of a miniaturized sensor system integrated into an autonomous underwater vehicle (AUV) for real-time acquisition of water quality parameters. The main application field of the presented system is the analysis of the discharge of nitrates into Norwegian fjords near aqua farms. The presented system was developed within the research project SALMON (Sea Water Quality Monitoring and Management) over a three-year period. The development of the sensor system for water quality parameters represented a significant challenge for the research group, as it was to be integrated in the payload unit of the autonomous underwater vehicle in compliance with the underwater environmental conditions. The German company -4H- JENA engineering GmbH (4HJE), with experience in optical in situ-detection of nutrients, designed and built the measurement system. As a carrier platform, the remotely operated vehicle (ROV) `CWolf` from Fraunhofer-Institut für Optronik, Systemtechnik und Bildauswertung - Institutsteil Angewandte Systemtechnik (IOSB-AST) modified to an AUV was deployed. The concept presented illustrates how the measurement system can be integrated easily into the vehicle with a minimum of hard- and software technical interfaces.