This paper presents a fault tolerant navigation system for a remotely operated vehicle (ROV). The navigation system uses hydro-acoustic position reference (HPR) and Doppler velocity log (DVL) measurements to achieve an integrated navigation. The fault tolerant functionality is based on a modified particle filter. This particle filter is able to run in an asynchronous manner to accommodate the measurement drop out problem, and it overcomes the measurement outliers by switching observation models. Simulations with experimental data show that this fault tolerant navigation system can accurately estimate the ROV kinematic states, even when sensor failures appear frequently.