We examined the effect of nutrients and grazers on Thalassia testudinum in Jobos Bay, Puerto Rico by fertilizing sediment and manipulating grazer abundances. Bottom-up effects were variable: Added nutrients did not increase seagrass aboveground biomass, but decreased belowground biomass-perhaps as a result of less biomass being allocated to belowground structures in response to greater nutrient supply in porewater. Experimental fencing of 1.5×1.5 m plots provided shelter that attracted large aggregations of fish, including seagrass herbivores. Seagrass biomass and shoot density decreased with increasing abundance of herbivorous fish, indicating a significant topdown effect. There were interactions between nutrient supply, provision of shelter, and grazing pressure. Fertilization enhanced seagrass %N; however, %N also increased in unfertilized plots that were fenced, most likely due to uptake of N excreted from the large numbers of fish associated with the fences. Only plots where shelter was provided and fertilizer was applied to sediments exhibited evidence of heavy grazing, reducing both seagrass cover and aboveground biomass. In the unfertilized fenced plots, signs of grazing were fewer despite large abundances of fish and enhanced nutritional quality of seagrass leaves. This suggests the possibility that high nutrient availability in sediments lowered concentrations of chemical defense compounds in the seagrass and that cues other than %N may have been involved in stimulating grazing. This study highlights the complexity of bottom-up and top-down interactions in seagrass systems and the important role of refuge availability in shaping the relative strengths of these controls.