Millennium is considered one of the few remaining coral reef ecosystems in the world that is relatively pristine. Inside the lagoon, the dominant corals are branching Acropora, forming plentiful patch and line reefs. These reefs likely provide important nursery habitat for important fisheries species like the blacktip reef shark (Carcharhinus melanopterus) and Napoleon wrasse (Cheilinus undulatus). Both species are heavily exploited throughout the Pacific, the Napoleon wrasse being under consideration for listing under the Endangered Species Act. However, they are abundant at Millennium.
While the large fishes are some of the most striking underwater and contribute to the large fish biomass on the reef, notably 4 out of every 5 fish on the reef are damselfishes. These relatively small-bodied fish are found amongst the fingers of the abundant Acropora corals. The whitetail dascyllus (Dascyllus aruanus) accounts for 35% of all fish in the lagoon.
Macroalgal cover in the lagoon is low, likely due to the large number of herbivorous (plant-eating) fishes and urchins and competition for space with corals. On the reef crest that is exposed during low tide, crustose coralline algae, a pink calcifying algae that glues the reef together) and turf algae are present.
The lagoon also hosts a large number of giant clams (Tridacna maxima), with an average of 3.5 clams per square meter in the north central regions. The southern part of the lagoon was reported to have an average of 35 clams per square meter in an 1988 expedition and indeed was found to have one area of 100% clam cover in 2009. However much of this area was littered with dead clam shells, possibly due to human poaching or aerial uplift of the island, leaving the shallow clams too far out of the water to survive.
Reef development inside Millennium lagoon are due to the dynamic growth and erosion processes, likely punctuated by changes in sea level and disturbance over thousands of years. As the reefs inside the lagoon grow, pillars of calcifying corals and algae have grown together, forming saddles. The result is a reticulate reef formation, which further influences water flow inside the lagoon. Notably, these pillars often grow east to west, which provides animals that eat plankton out of the water column with the greatest access to their food supply.
The outside of the island is surrounded by fringing reef. The windward side, exposed to frequent and large Pacific swells, has reef that rapidly slopes off from shore. The reef on the leeward side begins as a reef terrace that later turns into a steeper reef slope.
Among the animals and plants on land at Millennium Atoll are plants and animals on land are the coconut crab (Birgus latro), named for its ability to crack open coconuts with its claws and Pisonia grandis, a species of flowering tree in the Bougainvillea family. Coconut crabs can grow to be 70 cm in body length (not including legs), have a leg span of 1 m, weigh a few kilograms (with some estimates over 4 kg), and live for decades. Because of their large size and their fabled taste, the coconut crab has been harvested extensively from the inhabited Line Islands. However, remnant populations of crabs thrive on the uninhabited islands with population estimates of hundreds of thousands to millions of crabs.
Pisonia can form dense forests up to 20m in height and provide nesting habitat for a variety of seabirds. Once felled, their wood is relatively weak and rots quickly. While these forests were once abundance throughout the Pacific, in many locations with human habitation they have been replaced with nonnative coconut palms. These non-native coconut palms are also evident on Millennium, left over from a brief fifteen-year attempt by S.R. Maxwell and Company to export copra (dried coconut meat) before the company went into debt.
There are two particularly large populations of nesting seabirds on Millennium. Sooty Terns (Onychoprion fuscata), number about 500,000 individuals largely on the eastern islets of the atoll and Great Frigatebirds (Fregata minor) number approximately 10,000.