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Reefs in Southeast Asia, such as those in Indonesia’s Riau archipelago, are among the most diverse habitats in the sea, but limited baseline data pose a severe challenge for their conservation. Here, we surveyed five reef sites along the northern coast of Bintan Island to determine the most recent condition of the benthic and fish communities. Fourteen years of resort development on the island have elapsed since the last survey in 1993. Using several diversity measures to compare the reefs then and in 2007, we found that abundances of hard corals and fish remained high (average of >50% coral cover and >0.7 fish/m3), but taxonomic richness was compromised. The most common taxa now account for greater proportions of fish counts at all sites and of coral cover at three of four comparable sites. These shifts in coral and fish assemblages may be explained by freshwater influences and development along the north coast of Bintan Island. Because the local community and tourism industry still rely heavily on the reefs, we advocate implementing a comprehensive, integrated coastal management plan that mitigates further reef declines and promotes sustainable use.