Variable air volume (VAV) air handling unit (AHU) systems are the most common heating, ventilation, and air conditioning (HVAC) configuration in North America's commercial buildings. They account for a large fraction of sensors and actuators and are prone to faults due to their control systems' complexity. This research fills the gap in VAV AHU fault detection and diagnostics (FDD) through four parts. First, inverse model-based virtual sensors are developed to detect actuator faults in AHUs. Three algorithms are explored to compensate for the lack of reliable intermediate sensor data for five AHUs. Results indicate that although generated models can act as virtual sensors to identify hard faults, they cannot isolate faults' root causes. To address this uncertainty, the second part introduces a holistic sequential hierarchical FDD framework considering the significance of zone-to-system hard and sequencing logic fault interactions in AHUs and VAVs. The proposed framework follows this fault-checking order: AHU hard faults, VAV hard faults, AHU sequencing logic faults, and VAV sequencing logic faults. Faults are detected by visualizing the discrepancies between the expected and measured operational behaviour. The third part focuses on VAV AHU control systems (sensors, actuators, and sequencing logic), studying human errors during design, installation, and operation. Human errors are identified through a literature review and interviews with control specialists. The most common errors are classified, and interview examples are listed for different building life cycle phases. Since a commonly reported error by interviewees is thermostat misplacement, resulting in negative impacts on AHU supply air temperature (SAT) setpoint, the last step of this research investigates the robustness of sequences of operation to such errors. Fault tolerance of the most vulnerable sequences: SAT setpoint, duct static pressure (DSP) ix