Coral reefs are among the most diverse and productive ecosystems on the planet but are also significantly threatened by numerous natural and anthropogenic disturbances. Phase shifts or alternate stable state transitions where reef building corals are replaced by fleshy algae have become more and more common. While large scale global impacts such as climate change are clearly important, local impacts such as overfishing and nutrient pollution can also alter community dynamics. The relative importance of these top-down and bottom-up controls on reef community structure have been debated by scientists for years. Thus my goals were to test the independent and interactive effects of nutrient enrichment and herbivore exclusion on benthic community structure on a healthy reef in Hawaii and to follow this empirical approach with a global meta-analysis. My results show that both nutrients and herbivores are important in regulating benthic community structure but more importantly, they do so in different ways. Herbivores tend to reduce fleshy algal abundance while promoting the abundance of calcifying algae and coral. Nutrient enrichment alone tends to enhance algal growth rates but not necessarily abundance as herbivores can often consume this extra production. Finally the simultaneous effects of herbivore removal and nutrient enrichment lead to different benthic assemblages, largely dominated by fleshy algae. Thus, results from both empirical and meta-analytic approaches suggest that overfishing and nutrient pollution are important to the management and future conservation of coral reefs.