Eutrophication is a widespread phenomenon that disrupts natural ecosystems around the globe. Despite the general recognition that ecosystems provide many services and benefits to humans, little effort has been made to address how increasing anthropogenic eutrophication affects those services. We conducted a field experiment to determine the effect of nutrient enrichment on five ecological services provided by a model coastal system, a shallow seagrass community near Mobile Bay, Alabama (USA): (1) the provision of shelter for fauna; (2) the quality of food provided to first-order consumers; (3) quantity of food provision to first-order consumers and O2/CO2 exchange; (4) producer carbon and nitrogen storage, and (5) water clarity. The results showed a severe negative impact on seagrass density and biomass, which greatly reduced the structural complexity of the community and provision of shelter to fauna. Water clarity and the standing stock of producer carbon were reduced in the fertilized area in comparison with the control area. In contrast, nutrient addition did not affect in any consistent way the total quantity of food available for first-order consumers, the net exchange of O2/CO2, or the standing stock of producer nitrogen in the community. The nutritional quality of the food available for first-order consumers increased with fertilization. These results show that the impacts of nutrient enrichment on the services provided by natural systems may be disparate, ranging from negative to positive. These findings suggest that management policies for anthropogenic eutrophication will depend on the specific ecosystem service targeted. In the case of shallow seagrass beds, the loss of biogenic habitat and drastic impacts on commercially important fauna may be sufficiently alarming to warrant rigorous control of coastal eutrophication.