Due to the demands of booming Chinese cities and the increase in urban residents, the safety of aqueduct water transportation structures is noteworthy. A lot of old aqueducts were built in the 1990s and even earlier in the last century and may become vulnerable to potential earthquakes. This paper deals with an evaluation of an aqueduct’s seismic vulnerability accounting for leakage risk. Based on the Hua Shigou aqueduct in Ningxia, a probabilistic investigation was carried out to obtain the seismic fragility using Latin hypercube sampling. In the numerical study, the superstructure and substructure of the aqueduct were modeled as beam elements, and the lumped mass method was adopted to simulate the fluid–structure interaction. The rubber water stop’s mechanical performance was studied, and its damage states were proposed. Parametric numerical models were then subjected to a set of ground motions according to incremental dynamic analysis (IDA), which contained probabilistic parameters such as water, concrete strength, and bearing performance degradation. Both the system and component levels of the old aqueduct’s seismic fragility curves were obtained. It was found that the probability of the water stop’s leakage risk is significantly elevated with the increase in ground motion.
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