Autonomous systems are expected to maintain a dependable operation without human intervention. They are intended to fulfill the mission for which they were deployed, properly handling the disturbances that may affect them. Underwater robots, such as the UX-1 mine explorer developed in the UNEXMIN project, are paradigmatic examples of this need. Underwater robots are affected by both external and internal disturbances that hamper their capability for autonomous operation. Long-term autonomy requires not only the capability of perceiving and properly acting in open environments but also a sufficient degree of robustness and resilience so as to maintain and recover the operational functionality of the system when disturbed by unexpected events. In this article, we analyze the operational conditions for autonomous underwater robots with a special emphasis on the UX-1 miner explorer. We then describe a knowledge-based self-awareness and metacontrol subsystem that enables the autonomous reconfiguration of the robot subsystems to keep mission-oriented capability. This resilience augmenting solution is based on the deep modeling of the functional architecture of the autonomous robot in combination with ontological reasoning to allow self-diagnosis and reconfiguration during operation. This mechanism can transparently use robot functional redundancy to ensure mission satisfaction, even in the presence of faults.