Global Navigation Satellite Systems (GNSS) are used to provide accurate position, navigation, and time (PNT) information to users in various sectors of our society including transportation. Augmentation systems such as differential GNSS (DGNSS), real-time kinematics (RTK), and Precise Point Positioning (PPP) improve the GNSS performance, and providing reliable measurements from its reference station is very crucial. To ensure safe and accurate PNT solutions, code and carrier measurements must be monitored for potential faults or a performance degrade. Although there exist numerous methods to model and monitor the measurements, research on the carrier phase measurements is not as extensive as the code measurements. This paper introduces a split of residuals into receiver noise and multipath components to customize their estimation according to their respective statistical properties. This study also proposes a method to use machine learning-based non-linear regression to effectively model and monitor potential faults in the GNSS measurements including the carrier phase. A training dataset is used to model the nominal quantities of GNSS measurement residuals, and inflation factors are applied to over-bound the fault-free residuals. These inflated residuals are coupled with uncertainty factors to compute thresholds for monitoring carrier phase residuals, and the effectiveness of the thresholds is validated with a test dataset by achieving the false alarm rate of 6.61×10−6, slightly lower than the desired level of 10−5.