Clean Sea (Continuous Long-term Environmental and Asset iNtegrity monitoring at SEA) project [Gasparoni et al., 2013a] concerns the use of commercially AUV [Gasparoni et al., 2013b] with a modular interchangeable payload for environmental monitoring and inspection tasks around Eni oil & gas offshore infrastructures. The platform identified for the development of the project was SAAB Seaeye Sabertooth. The project defined peculiar hardware and software architecture, where the payload controller is separate from the AUV controller and able of modifying “in real time” the mission strategy [Buffagni et al., 2014]. The environmental payload chosen for AUV was: Temperature [°C], Salinity [psu], Methane [μmol/l], Colored Dissolved Organic Matter [ppb], Chlorophyll [μg/l], Turbidity [m-1...