In order to resolve the challenges in the investigation and decision-making regarding the water leakage and seepage problems of operational tunnels in karst areas, namely ambiguous geological information and high acquisition costs, as well as difficulty in tracing the causes and low treating efficiency, a qualitative analysis method based on the conceptual model of karst groundwater movement is proposed. This method constructs a four-stage conceptual model of recharge-runoff-discharge-damage. It integrates the core elements of the four stages and clearly defines the correlation mechanism between each stage and damage. Simultaneously, a three-tier analysis framework of macro-meso-micro is established. At the macro level, the relationship between the groundwater migration path and the concentrated damage sections is analyzed. At the meso level, the connection between the technical condition of drainage facilities and the damage is examined. At the micro level, the association between structural defects and seepage is investigated. Moreover, the missing geological information is supplemented by inferring from the characteristics of the damage. Relying on a long tunnel project in Guangxi, China, the models are conducted on two typical sections. It is determined that in section A, concentrated water inrush occurs during the rainy season due to the presence of karst conduit flow, while in section B, uniform dripping is presented due to the dominance of fissure flow. Targeted treatment plans are designed. After one-year follow-up verification, it is found that the water leakage and seepage damage have been significantly alleviated. The corresponding relationship between the four stages of karst groundwater movement and the water leakage and seepage damage of tunnels is clarified and the proposed conceptual model provides a approach for the investigation, analysis, and decision-making of water leakage damage.