The vivid colors on the north shores of the Ayamaru Lakes are the result of pigmented bacteria in the microbial mats that grow around the edges of the mineral-rich water.

The bacteria produce colors ranging from orange to red; the amount of color in the microbial mats depends on the ratio of chlorophyll to carotenoids and on the temperature of the water, which favors one bacterium over another.

Most of the wildlife is found in the wetlands along the southern shores of Lake Ayamura.

There are four endemic fishes in the lakes, the Ajamaru Lakes rainbowfish (Melanotaenia ajamaruensis), Boeseman's rainbowfish (Melanotaenia boesemani), Vogelkop blue-eye (Pseudomugil reticulatus) and Hoese's goby (Glossogobius hoesei).

Non-endemic natives include the shortfin tandan (Neosilurus brevidorsalis) and fimbriate gudgeon (Oxyeleotris fimbriata), while several other fish species have been introduced by humans.