Nutrient pollution alters the metabolic compatibility between symbionts and coral hosts, which increases bleaching susceptibility and incidence of disease. However, little is known about the molecular interactions between the coral host and its microbial partners that contribute to holobiont responses to nitrogen pollution. Further, while it has been suggested that holobiont responses to nutrient pollution can be reversible, it is yet to be seen if these effects can carry-over to the next generation. To test this, colonies of brooding, vertically transmitting stony corals in the genus Pocillopora were enriched with excess nitrate in situ for one year and allowed to naturally planulate. Holobiont traits, coral host gene expression, and microbial communities (Symbiodiniaceae and bacteria) were characterized in adults before and after planulation as well as in planula from a subset of adults. Although host colonies were separated by >10 m, clonality and chimerism were observed in the majority of colonies. Thus, both lineage- and treatment-specific effects of nitrate treatment on coral host gene expression were detected. This included enrichment of functional categories of genes associated with the synthesis of nitrogenous compounds, which likely contribute to fine-scale tuning of micronutrient exchange within the holobiont. Compositional changes to bacterial communities were detected at the end of the enrichment period, but these differences dissipated after the removal of nitrate and after planulation. While Symbiodiniaceae and bacterial communities varied between adults and planula, we observed no carry over effects of nitrate treatment in the planula, suggesting coral host responses to nutrient pollution in the field are likely transient and potentially reversible.