In this paper, a methodology is developed to ensure the integrity of navigation systems given that the measurement noise characteristics might change under different environments. For demanding aviation applications such as autonomous shipboard landing or autonomous airborne refueling, accuracy and integrity of carrier phase positioning and cycle resolution are essential. Integrity risk is computed from the estimate error covariance matrix, which is ultimately derived from the measurement noise covariance matrix. Therefore, any changes in the noise characteristics must be properly accounted for in the integrity risk computation. In this work, a monitor that detects sudden increases in the noise variance is proposed along with an explicit quantification of its effect on integrity risk.