Human activity and natural climate trends constitute a major threat to coral reefs worldwide. Models predict a significant reduction in reef spatial extension together with a decline in biodiversity in the relatively near future. In this context, monitoring programs to detect changes in reef ecosystems are essential. In recent years, coral reef mapping using remote sensing data has benefited from instruments with better resolution and computational advances in storage and processing capabilities. However, the water column represents an additional complexity when extracting information from submerged substrates by remote sensing that demands a correction of its effect. In this article, the basic concepts of bottom substrate remote sensing and water column interference are presented. A compendium of methodologies developed to reduce water column effects in coral ecosystems studied by remote sensing that include their salient features, advantages and drawbacks is provided. Finally, algorithms to retrieve the bottom reflectance are applied to simulated data and actual remote sensing imagery and their performance is compared. The available methods are not able to completely eliminate the water column effect, but they can minimize its influence. Choosing the best method depends on the marine environment, available input data and desired outcome or scientific application.
