Rover missions typically involve visiting a set of predetermined waypoints to perform science functions, such as sample collection. Given the communication delay between Earth and the rover, and the possible occurrence of faults, an autonomous decision making system is essential to ensure that the rover maximizes the scientific operations performed without damaging itself further or stalling. This paper presents a modular software architecture for autonomous decision making for rover operations that uses diagnostic and prognostic information to influence mission planning and decision making to maximize the completion of mission objectives. The decision making system consists of separate modules that perform the functions of control, diagnosis, prognosis, and decision making.We demonstrate our implementation of this architecture on a simulated rover testbed.