Incubation studies were conducted with pre-filtered reef seawater microbial communities to monitor the response of microorganisms to exudates released from two species of corals (Porites astreoides and Gorgonia ventalina) and three specific metabolites including caffeine, pantothenic acid, and riboflavin. The results of these incubation studies place the importance of benthic exudates and metabolites into an ecological context and help us understand benthic-pelagic feedbacks in coral reef ecosystems.