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Prediction study of karst water bursting is one of the key problems that need to be solved among engineering geological prospecting. It is too difficult to predict karst water bursting in covered karst region due to the limitation of prospecting methods and prediction theories now. It is taken as a case study of Guangzhou Rail Transit Line No.9 project, which passes through covered karst region. The depth of the tunnel is deep to the bedrock or near the bedrock surface, therefore there may exist risks of water bursting problem. Because there exist hydraulic connections to different degrees between different kinds of voids of different scales in karst aquifer medium, whether it is directly disclosed by drilling of the karst cave system possibly leading to karst water bursting, or not, the bursting point must have a close relationship to vertical flow, temperature anomaly and groundwater level fluctuating, etc. Based on this point, comprehensive analysis methods is used in this paper, which are groundwater vertical flow testing, groundwater temperature field analysis, groundwater level fluctuation monitoring and karst cave statistics exposed by drill and so on. Two karst water bursting locations were founded in the bid section A of the project finally. In addition, three kinds of water bursting patterns are defined, namely, water bursting of karst pipeline system, water bursting of local cave, and combined water bursting of karst cave or karst pipeline system connecting overlying permeable sand layer.