This paper presents the design and development of an Autonomous Amphibious Unmanned Aerial Vehicle (AAUAV) System with hybrid version of a Multicopter and a Hovercraft that can vertically take-off and land as well as travel on water and smooth earth surfaces for water based applications like water quality assessment, water sampling, remote sensing, underwater mapping etc. Based on the conceptual design, parameters such as aircraft overall dimensions, weight estimation, aircraft performance, power requirement and endurance of the UAV were calculated and evaluated. Using these computed parameters, a suitable propulsion system was selected. A 3D CAD model of the UAV was developed and 2D manufacturing drawings were made. Finally, a prototype of the UAV was fabricated, assembled, and all the sub-systems were integrated. Initial trial runs were made to check the proper functioning of all sub-systems as intended. Subsequently, to verify and validate the UAV’s concept and design configuration, ground and field tests were conducted to test the vertical-take-off and landing, flying, and amphibious capabilities of the developed unmanned system. Results of the tests have proven that a well-conceived Design and development has been successfully completed.