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Limited energy is one of the principal challenges in Wireless Sensor Networks (WSNs). In the application of Structural Health Monitoring (SHM), overwhelming data provision is another big problem. Data aggregation condenses raw data into useful information and reduces redundant data transmissions. Consequently, significant energy and data storage are saved, and tasks can be completed more efficiently. However, it is a nontrivial problem to organize the various data aggregation techniques into an integrated architecture on a distributed WSN. In this paper, we propose a cluster-based data aggregation architecture to facilitate application development for efficient SHM. We developed a role-based data aggregation middleware and SQL-like user interface to support flexible task configurations. We also implemented a prototype to evaluate operational flexibility and energy efficiency. Our experimental results indicate that a cluster-based data aggregation mechanism can save energy and optimize the distribution of computing tasks.