This paper describes an open source navigation system architecture for use in autonomous underwater vehicles. It is based on the Mission Oriented Operating System proposed, published and programmed by (Newman (2006), Newman (2008)). It is uniquely applicable for work-in- progress type and development-stage software and capability installation onto an AUV system. This applicability is achieved by its completely modular nature, which is obtained by the operating system kernel running separate processes for each advanced navigation or control feature. Robustness is also achieved in this respect since failures and errors will cause only the individual modules that incurs them to fail. Such critical errors, bugs and failures will thereby be contained and their propagation halted from completely freezing even the low-level control loops and decision- making processes needed to successfully retrieve the malfunctioning AUV.