A generic method was developed for analysing the capabilities of optical remote sensing of aquatic systems in terms of environmental components and imaging sensor configurations. The method was based on a component based model of the entire system in which not only benthic composition but other environmental components such as water inherent optical properties (IOPs), bathymetry, sun elevation, wind speed and sensor noise characteristics were defined by datasets with the potential to include across-image variation. The model was applied to data from Pacific Ocean reefs in an airborne sensor context to estimate the primary environmental or sensor factors confounding discrimination of benthic mixtures of key reef types: live coral, bleached coral, dead coral and macroalgae. Results indicate that spectral variation of benthic types and sub-pixel mixing is the primary limiting factor for benthic mapping objectives, whereas instrument noise levels are a minor factor.