Local-scale nutrient pollution can alter coral growth and reproductive output, as well as their resident communities of microorganisms (dinoflagellates in the family Symbiodiniaceae, bacteria). Yet, the ways in which nutrient pollution alters coral interactions with their microorganisms are not fully understood, and no studies have tested for transgenerational impacts of nutrient stress on coral holobionts. To investigate this, colonies of Pocillopora acuta were enriched with nitrate in situ for up to one year and monitored for planulation. Gene expression, resident microbial communities and holobiont traits were characterized in adults, as well as in planulae. Although separated by > 5 m, clonality and chimerism were observed in the majority of coral colonies. Lineage and treatment-specific effects of nitrate treatment were detected in adults and planulae. Nitrate-enriched adults contained higher densities of Symbiodiniaceae and exhibited downregulation of genes involved in the synthesis of nitrogenous compounds. Planulae harbored higher Symbiodiniaceae and bacteria diversity than adults; this study constitutes the first assessment of these microorganisms from individual planulae. Coral-associated bacteria communities were Endozoicomonas-dominated and were not altered by nutrient treatment. Planula-associated bacteria communities differed from their parents but not from parental exposure to nutrients, and no changes in fecundity or settlement success resulted from enrichment. Taken together, these findings suggest that adult corals acclimate to chronic nutrient pollution by harboring higher Symbiodiniaceae densities, with no observed negative effects on the subsequent generation.