In this paper we discuss about the design and development of an “Autonomous Amphibious Unmanned Aerial Vehicle (AAUAV)” that can fly autonomously to the polluted water areas where human accessibility is formidable to test the water quality. The AAUAV system is an integrated multi-copter with tilt rotor capability to facilitate easy landing, navigation and maneuver on water. A 3D CAD model has been designed and analyzed. A specific propulsion system has been devised and lab tested. A proof of concept model has been made and tested in the field with its instruments to ascertain its technical/ operational feasibility. This system can also be tailored to collect and store the water samples from the polluted sites for further comprehensive research at the laboratory. AAUAV system is the novel solution to the polluted environment through a complete integrated system. This will be an effective alternative for the conventional water sampling techniques.