This paper presents a robust strategy for online fault detection and optimal control of condenser cooling water systems. The optimal control strategy is formulated using a model-based approach, in which simplified models and a hybrid quick search (HQS) method are used to optimize the performance of the overall system by changing the settings of the local process controllers. A system level online fault detection scheme is embedded into the control system and used to monitor whether the system operates in a healthy condition. The faults considered are mainly the component performance degradations. When a fault is detected, the control system will be reconstructed to regain the control through using robust schemes. The performance of the proposed strategy is tested and evaluated against on a simulated virtual system representing the actual condenser cooling water system in a super high-rise building. The results show that the fault detection scheme is effective in identifying system performance degradations and the fault-tolerant control strategy with online fault detection and optimal control can enhance the overall system performance significantly when the operation of condenser cooling water systems suffers from performance degradations, as compared to that using optimal control only.