Predators can influence the structure and function of ecosystems by altering the composition or behavior of herbivore communities. Overexploitation of predators, therefore, may lead to habitat loss by altering important top-down interactions that facilitate habitat-forming species. In seagrass beds, top-down control of algal growth by mesograzers appears to facilitate seagrass production. The indirect consequences of higher-order trophic interactions, however, remain unclear. Although predators may limit the beneficial effects of algal mesograzers, it is also possible that they limit the abundance of invertebrates that consume and foul seagrasses. We used experimental enclosure and exclosure cages to explore the direct and indirect effects of microcarnivorous fishes on epifaunal invertebrates, epiphytic loads, and seagrass growth in a natural eelgrass (Zostera marina) bed in San Diego Bay, California, USA. Contrary to expectations, when fishes were excluded, invertebrate abundance increased by 300-1000%, fouling on eelgrass leaves increased by 600%, and eelgrass production declined by 50%. Despite high densities of predators in enclosures, subsequent effects did not differ from ambient conditions. When predators were excluded, however, abundances of epifauna (including tube-building crustaceans and an eelgrass-grazing limpet) increased dramatically, resulting in reduced seagrass production. Our results are supported by several studies of eelgrass communities in the northeastern Pacific, characterized by coastal upwelling, inverse estuaries, and a voracious seagrass-consuming limpet. These strong, positive, indirect effects of microcarnivores on seagrass production contrast with the beneficial mesograzer paradigm, highlighting the need for hypotheses to be tested across a variety of ecosystems with varying biophysical characteristics.