Ocean warming has severe impacts on coral reef ecosystems with frequent incidences of coral bleaching. In addition, eutrophication poses an increasing threat to coral reef environments and has been found to increase the vulnerability of corals to thermal bleaching. Eutrophication has accelerated in recent years with coastal nutrient loads expected to continue to increase under global change. However, the mechanisms by which nutrient pollution affects corals and coral reefs are still under debate, in particular with regard to nitrogen. The main objective of this paper is to review mechanisms by which nitrogen pollution affects coral health and corresponding strategies to reduce the impact of nitrogen pollution. Different coral species possess varying tolerance thresholds for nitrogen enrichment and corals show differential responses to enrichment with nitrate and ammonium. Nitrate assimilation increases oxidative stress in corals, promotes growth of the phototrophic symbionts in corals, and induces phosphate starvation in these symbionts, which further impairs the symbiosis. In contrast, a moderate supply of ammonium is mostly beneficial for coral development. In addition, combined nitrogen and phosphorous enrichment can indirectly compromise coral health by enhancing macroalgae growth and increasing the incidence of coral diseases caused by predation on corals. It must be realized that both levels of nutrient pollution and the stoichiometric ratios of C: N: P: Fe availabilities determine the ultimate effect of nutrients on coral health. We confirm the strategy to conserve coral reefs via coral-targeted water quality management, in particular by including a reduction of the nitrate influx and by proper management of fish stocks to facilitate healthy reef ecology.