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Coral reefs are experiencing increasing disturbance regimes. The influence these disturbances have on coral reef health is traditionally captured through field-based monitoring, representing a very small reef area (<1%). Satellite-based observations offer the ability to up-scale the spatial extent of monitoring efforts to larger reef areas, providing valuable insights into benthic trajectories through time. Our aim was to demonstrate a repeatable benthic habitat mapping approach integrating field and satellite data acquired annually over 21 years. With this dataset, we analyzed the trends in benthic composition for a shallow platform reef: Heron Reef, Australia. Annual benthic habitat maps were created for the period of 2002 to 2023, using a random forest classifier and object-based contextual editing, with annual in situ benthic data derived from geolocated photoquadrats and coincident high-spatial-resolution (2–5 m pixel size) multi-spectral satellite imagery. Field data that were not used for calibration were used to conduct accuracy assessments. The results demonstrated the capability of remote sensing to map the time series of benthic habitats with overall accuracies between 59 and 81%. We identified various ecological trajectories for the benthic types, such as decline and recovery, over time and space. These trajectories were derived from satellite data and compared with those from the field data. Remote sensing offered valuable insights at both reef and within-reef scales (i.e., geomorphic zones), complementing percentage cover data with precise surface area metrics. We demonstrated that monitoring benthic trajectories at the reef scale every 2 to 3 years effectively captured ecological trends, which is crucial for balancing resource allocation.