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A significant number of high spatial resolution (4 m) Ikonos images acquired over shallow coastal environments present quasi-stochastic sea surface effects that seriously compromise reconnaissance of bottom features. This problem is common in wide field-of-view images where there is limited control on acquisition conditions other than cloud cover. To eliminate most of these wave and glint patterns, we use the near-infrared band, which exhibits maximum absorption and minimal water leaving radiance over clear waters, to characterize the spatial distribution of relative glint intensity, which is then scaled by absolute glint intensities in each of the visible bands. The result is subtracted from the visible bands, thus filtering out glint effects. Corrected visible bands clearly reveal seabed structural features obscured in the original data. Before- and after-correction classifications of an Ikonos image of Lee Stocking Island (Bahamas) reveal an improvement of user's accuracies for critical benthic habitat classes such as coral-dominated habitat (46.8% versus 60.5%) or dense seagrass beds (31.7% versus 52.1%). This technique offers potential to use previously discarded sections of high spatial resolution airborne or satellite images of optically shallow water for mapping substrate features.