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With the development of computer network technology, overlay network technology is increasingly widely concerned. Aiming at many problems encountered in water environment monitoring, this paper mainly discusses the methods how to efficiently achieve the water environment monitoring and warning in the area of the special geographical environment and climate by online real-time monitoring system of water environment based on overlay network technology. Especially, we integrate the ETL process with the spatial database to analyze and process the complex heterogeneous data. Furthermore, we design a new network topology of the sensor node according to the characteristics and area of the water in Wuliangsuhai for the efficient application of real-time monitoring system of water environment based on overlay network technology in cold and arid region. Subsequently, this framework and network topology has been put into use in Wuliangsuhai for the on-line real-time water monitoring tests. The results show that the overlapping network architecture is feasible, network topology of the sensor node plays a key role for data acquisition and on-line analysis and early warning of heterogeneous data is efficient. Henceforth, we will further research on how to construct the more practical data analysis model of multidimensional cloud calculation and extended the applications.