Stony corals are the foundation species of tropical reefs, and their structures can harbor a diverse range of mutualist taxa that can confer important benefits, including provision of nutrients. Prominent among the associates of branching coral in the genus Pocillopora are groups of zooplanktivorous damselfishes that take refuge in the coral to avoid their predators. In field and laboratory experiments, we explored the effects of colonies of resident damselfishes on growth of their host corals. Laboratory studies revealed a positive relationship between biomass of fish and output of ammonium. In the field, levels of ammonium were significantly elevated in the water surrounding the branches of Pocillopora occupied by colonies of damselfish, particularly in time periods following active feeding by the fish. Experimental manipulation of the presence of fish on host corals during a month-long field experiment revealed that corals hosting fish grew significantly more than those that lacked fish, and coral growth was positively correlated with the biomass of resident fish. The Pocillopora colonies in the field experiment varied in the degree of openness of their branching structure, and dye studies indicated that this affected their ability to retain waterborne nutrients. Together with biomass of resident fish, colony openness explained 76% of the variation in coral growth rate during the experiment. Corals can exhibit considerable morphological variability, and mutualistic fish respond to colony architecture during habitat selection, with some species preferring more open-branched forms. This makes it likely that corals may face tradeoffs in attracting resident fish and in retaining the nutrients they provide.