The fundamental components of a coral reef are coral, algae, and sand. At its simplest assessing the status of a coral reef may be reduced to quantifying the relative benthic cover of these three bottom-types. While in situ surveys can provide an accurate census on an individual reef scale (10s of meters), the only feasible method to surveys coral reefs on a reef tract (10-100s of kilometers) or worldwide scale is through the use of remote sensing. Remote sensing is a means of surveying entire ecosystems. A major issue in remote sensing of coastal environments is the confounding effects of the water column on the signal emerging from the water column. We used a simulation method to model differing levels of environmental parameters, which occur in marine ecosystems, with HydrolightEcolight 5. Simulated data were interpolated with actual bottom; type spectra to determine the accuracy of a classification function developed in MATLAB. The aim was to distinguish bottom-types as well as predict levels of water column parameters. The results of this study demonstrate that bottom-type (78% algae, 84% coral, and 94% sand) and chlorophyll concentration (85-90% across range) are well determined, while depth and suspended sediment load are not as well predicted (<70%) and has a tendency to slightly over predict depth.