Increases in ocean temperatures interact with spatially variable local stressors such as nutrient pollution to influence the prevalence and severity of coral bleaching. Nutrient pollution influences coral holobiont traits by altering the metabolic compatibility between symbionts and coral hosts. However, little is known about the molecular interactions between the coral host, symbiont community, and microbiome that contribute to the holobiont effects of nitrogen pollution as well as potential carry-over effects to the next generation. To test this, colonies of the brooding, vertically transmitting coral in the genus Pocillopora were enriched with excess nitrate in situ on the reef for one year and allowed to naturally planulate. Holobiont traits and coral host gene expression was characterized in adults as well as planula to address contributing factors of molecular disruption due to long-term nitrate exposure in the field. Despite substantial physical distancing between collected Pocillopora colonies, clonality and chimerism were observed. Thus, both lineage and nitrate treatment specific effects on coral host gene expression were detected. This included enrichment of functional categories of genes associated with the synthesis of nitrogenous compounds and heavy-metal binding, genes previously linked to fine-scale tuning of micronutrient exchange with algal symbionts. Further, while nitrate effects were detected in adults, little to no effect was observed in the planula, suggesting coral host responses to nutrient pollution in the field are likely transient and potentially reversible.