The invention relates to multi-level/multi-threshold/multi-persistency GPS/GNSS atomic clock monitoring. Methods and apparatus to monitor GPS/GNSS atomic clocks are disclosed. An example method includes establishing a measured difference between an atomic frequency standard (AFS) and a monitoring device. The method also includes modeling an estimated difference model between the AFS and the monitoring device, and computing a residual signal based on the measured difference and the estimated difference model. In addition, the method includes analyzing, by a first detector, the residual signal at multiple thresholds, each of the thresholds having a corresponding persistency defining the number of times a threshold is exceeded before one or more of a phase jump, a rate jump, or an acceleration error is indicated. Furthermore, the method includes analyzing, by a second detector, a parameter of the estimated difference model at multiple thresholds, each of the thresholds having a corresponding persistency defining the number of times a drift threshold is exceeded before a drift is indicated.