The Autonomous Surface / Sub-surface Survey System (ASSSS) research program combines long endurance autonomous surface vessels (ASVs) and long endurance autonomous underwater vehicles (AUVs) to create an integrated cooperative navigation system effectively transforming the capabilities and accuracy of AUV survey. ASV is leading the project, working alongside National Oceanography Centre, a world leading research center and developer of AUV systems, Sonardyne International a leading developer of subsea acoustic positioning, communications and sonar systems and SeeByte a developer of software solutions for autonomous systems. The system architecture enables an ASV to provide regular position updates to the AUV system removing the need for the AUV to surface from depth to update its internally calculated position, a Cooperative Localization Scheme will increase the efficiency and accuracy of AUV survey. With the combination of the high accuracy sonar systems positioned close to the seabed on the AUV and accurate position from the ASV this will provide game changing solutions. The ASV communicates with the AUV through 2 key methods; acoustics to provide short mission updates and positioning information and optical communication technology to enable the system to upload the data from the survey sensors. With the data uploaded to the ASV it is then possible for it to process this data to enable summary data to be passed back through satellite communications. Future projects will look at how the data processed onboard can be used to adaptively update the mission in situations where data may indicate further investigation is required. Due to the endurance and autonomy, this system will also bring the possibility of completing subsea operations from a shore base, without the need for ships to be mobilized, significantly reducing data acquisition costs and improving safety. This transition to autonomy will save cost, reduce risk, and increase flexibility across a range of applications including mine countermeasures, weapons testing, hydrography, environmental science, security, and surveillance.