We have established an Australia-wide observation program that exhibits recent developments in autonomous underwater vehicle (AUV) systems to deliver precisely navigated time series benthic imagery at selected reference stations on Australia’s continental shelf. These observations are designed to help characterize changes in benthic assemblage composition and cover derived from precisely registered maps collected at regular intervals. This information will provide researchers with the baseline ecological data necessary to make quantitative inferences about the long-term effects of climate change and human activities on the benthos. Incorporating a suite of observations that capitalize on the unique capabilities of AUVs into Australia’s integrated marine observation system (IMOS) [1] is providing a critical link between oceanographic and benthic processes. IMOS is a nationally coordinated program designed to establish and maintain the research infrastructure required to support Australia’s marine science research. It has, and will maintain, a strategic focus on the impact of major boundary currents on continental shelf environments, ecosystems, and biodiversity. The IMOS AUV facility observation program is designed to generate physical and biological observations of benthic variables that cannot be cost effectively obtained by other means.