This paper describes a mission outline and a design concept of an Autonomous Underwater Vehicle (AUV) for monitoring marine ecosystem and physical microstructures. The key point of this AUV development is to build a monitoring platform with low vibration at slow cruising speed, because the main target of the monitoring is the plankton environment with physical microstructures i.e. turbulences. For this need, the vehicle will be equipped with a newly developed water jet propulsion system. To increase an efficiency of the propulsion system, a duct is mounted covering the outlet of the water jet. The experimental date and the predictions were compared for the future design of AUV.