 This study developed a generic method for analyzing 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, which included benthic composition, water inherent optical properties, IOPs, bathymetry, sun elevation, wind speed, and sensor noise characteristics. This model was then 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 indicated that spectral variation of benthic types and sub-pixel mixing is the primary limiting factor for benthic mapping objectives, while instrument noise levels are a minor factor. This article was authored by John D. Headley, Chris M. Ralph-Sema, Peter J. Mumby, and others.