In this paper, we propose a novel bilinear observer- based robust fault detection, isolation and adaptive fault estimation methodology to precisely estimate a class of actuator faults, namely bias in damper position and lock-in-place faults, in Variable-Air-Volume (VAV) terminal units of Heating Ventilation and Air-Conditioning (HVAC) systems. The proposed adaptive fault estimator is robust in the sense that the fault estimates are not affected by the unmeasured disturbance variable and that the effects of measurement noises on fault estimates are attenuated. The fault estimation algorithm with the integrated building control system improves occupants comfort and reduces the operation, maintenance, and utility cost, thereby reducing the impact on the environment. The effectiveness of the methodology for adaptive estimation of multiple or single VAV damper faults is successfully demonstrated through different simulation scenarios with SIMBAD (SIMulator of Building And Devices), which is being used in industries for testing and validation of building energy management systems.