The sustained and cost-effective monitoring of the water quality within European coastal areas is of growing importance in view of the upcoming European marine and maritime directives, i.e. the increased industrial use of the marine environment. Such monitoring needs mechanisms/systems to detect the water quality in a large sea area at different depths in real time. This paper presents a system for the automated detection and analysis of water quality parameters using an autonomous underwater vehicle. The analysis of discharge of nitrate into Norwegian fjords near aqua farms is one of the main application fields of this AUV system. As carrier platform the AUV "CWolf" from the Fraunhofer IOSB-AST will be used, which is perfectly suited through its modular payload concept. The mission Task and the integration of the payload unit which includes the sensor module, the scientific and measurement computer in the AUV carrier platform will be described. Few practice oriented information about the software and interface concept, the function of the several software modules and the test platform with the several test levels to test every module will be discussed.