Successfully-operated low-nutrient and ultra-low-nutrient reef aquaria rely upon a balance of carbon, nitrogen, and phosphorus in order to enable beneficial microbes to efficiently remove latent organic material by means of consuming it and converting it into additional microbial biomass. The resulting supply of planktonic microbes is exported from the system via protein skimming and/or captured by corals and other suspension-feeding invertebrates, recycling organic material (waste) into additional biomass of these organisms.

These nutrients are also required by zooxanthellae for continued existence. The ability of microbes to remove nutrients from their surroundings relies upon the presence of adequate supplies of organic carbon, nitrogen, and phosphorus. The aquarist may employ appropriate filtration material to reduce the concentrations of these nutrients, however bringing the nutrient concentrations into balance will accomplish the same task.

Failure to maintain adequate nutrient content in any reef system may result in bleaching and/or tissue degradation of zooxanthellate invertebrates.