This study is purposed to develop an efficient fault detection method for Global Navigation Satellite Systems (GNSS) applications based on adaptive noise covariance estimation. Due to the dependence on radio frequency signals, GNSS measurements are dominated by systematic errors in receiver’s operating environment. In the proposed method, the pseudorange and carrier-phase measurement noise covariances are obtained at time propagations and measurement updates in process of Carrier-Smoothed Code (CSC) filtering, respectively. The test statistics for fault detection are generated by the estimated measurement noise covariances. To evaluate the fault detection capability, intentional faults were added to the filed-collected measurements. The experiment result shows that the proposed method is efficient in detecting unhealthy measurements and improves GNSS positioning accuracy against fault occurrences.