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Coral communities have attracted significant attention in the past decade in light of alarming global observations regarding a decline in their health. The synoptic spatial and temporal capabilities of remote sensing provide a valuable tool for the monitoring and assessment of these communities. This is particularly relevant given the inherent geographic distribution of coral reefs and the logistical difficulties associated with extensive in situ underwater observation. However, the confounding influences of both varying water column properties and the complex mosaics of coral species create many technical difficulties and physical limitations for applications of remote sensing in benthic habitats. Nevertheless, hyperspectral instruments, such as NASA's Airborne Visible InfraRed Imaging Spectrometer (AVIRIS), provide a promising technology for investigating this complex environment. Presented here is an empirical approach for calibrating water-leaving reflectance of hyperspectral imagery using natural underwater calibration targets. The analysis uses AVIRIS imagery acquired over Kaneohe Bay on Oahu in the Hawaiian Islands. We describe the methods employed to obtain benthic reflectance measurements of sand calibration targets within the bay using a GER 1500 portable spectrometer in a custom underwater housing.