Observer based stochastic disturbance accommodating control scheme utilizes an estimator to determine the necessary corrections to the nominal control input and thus minimizes the adverse effects of both model uncertainties and external disturbances on the controlled system. The total control input, which includes the nominal control as well as the control corrections to the nominal control to accommodate for the disturbances, could exceed the actuator saturation limits. The saturation of the disturbance accommodating control system is more violent than that of the nominal control system because of the positive feedback of the disturbance compensation. This paper presents the formulation of the stochastic disturbance accommodating controller with actuator saturation for a class of uncertain linear stochastic systems. A Lyapunov based stochastic adaptive approach is used to update the control gains and the process noise covariance online so that the closed-loop stability of the controlled system is guaranteed.