Developing a continuous and a real-time autonomous system for a long-term water monitoring is the goal of my research. A water monitoring system is for large rivers to improve the water quality and to keep track the condition of the river. For my research ‘Wabash River’ is the targeted test site because it is the one of the longest rivers in the US and main stream in Indiana state. There are many on-going researches for an autonomous water monitoring system. My research will be continuous, real-time and autonomous monitoring system. One of the scenario is utilizing a UAV and USVs collaboration team. UAV will fly over the ROI and take images, providing a real time global map for effective path planning of USVs. Base on the path planning, USVs will perform various tasks. USVs will send data which they collected via a real-time data transmission system. This research is at the beginning stage. Based on the needs assessment, this system will be iteratively designed to be fully capable of various tasks, such as water sampling, water pollution monitoring, sediment sampling, and early flood warning.