Monitoring of marine ecosystems is essential to understanding long-term ecological patterns and species diversity. Yet for fish communities on the east coast of Australia, continued monitoring on the Great Barrier Reef is generally limited to shallow coral reef environments and no measures are currently in place to monitor deep (20-80m) inter-reef waters. Deep-water inter-reef environments support fish assemblages of commercial, recreational, cultural, and ecological significance but are also vast and difficult to survey. In 2021, a multi-institutional Integrated Reef Fish Monitoring Program was developed to provide pathways for improved monitoring of these under-surveyed areas. Habitats such as submerged shoals, Halimeda banks, seagrass beds, and deep-water filter-feeder dominated communities were targeted for fish aggregations using multibeam sonar which fed into a spatially-balanced survey design to establish baselines for monitoring using stereo-BRUV and stereo-ROV sampling techniques. Preliminary results using multivariate and Bayesian analyses have shown this approach is an effective tool to capture distribution of fish assemblages and can be used for repeated monitoring. Unique spatial patterns in diversity were found for key fisheries species and broader fish community relative abundance. The inter-reef was also found to provide refuge for threatened species and host a strong diversity of fish uncommon to shallow-water survey, providing further justification for monitoring these areas into the future.