Ionospheric disturbances affect Global Positioning System (GPS) performance in terms of accuracy and integrity, especially over the equatorial region. During the period of the disturbances, GPS receivers suffer from a high noise level. Not taken into account by the current stochastic model, the ionospheric disturbances degrade GPS positioning accuracy. In addition, non-Gaussian tails are observed in the distribution of the noise during the period of the disturbances; therefore the integrity of GPS can also be affected. This paper develops a statistical solution that is able to mitigate effects of ionospheric disturbances on GPS accuracy and integrity using a commercial dual frequency receiver. The Rate of Total Electron Content (TEC) change Index (ROTI), a parameter derived from the dual frequency receiver, is used to group the levels of ionospheric disturbances. The standard deviations of the pseudorange noise under different groups are evaluated. By incorporating both the ROTI and the satellite elevation, a modified stochastic model is proposed to reduce the effect of the disturbed observation on the positioning accuracy. The performance of the model is evaluated by a test and an inflated sigma for each group is recommended for over-bounding anomalies of observations to protect the user against threats from ionospheric disturbances. This technique, together with results in this paper, can be applied to mitigate the effects of ionospheric disturbances on GPS.