Reef-building corals are sensitive to excessive nitrogenous (N) compounds. To maintain levels of inorganic nitrogenous compounds low in coral aquaria, various technologies, mechanical, chemical and biological, have been applied. As one of the biological techniques, “live rock,” which can be defined as a dead coral skeleton covered with crustose coralline algae (CCA), has long been applied for coral aquaria. Until recently, however, there has been little evidence for the effectiveness of live rock in removal of N compounds from coral aquaria. Demonstrating comparative experiments with live rocks, here we report that the live rock is capable of removing N compounds and reduces the mortality of reef-building coral. We cultured the reef-building coral Acropora digitifera with the sea cucumber Holothuria atra as a natural nitrogen producer. H. atra increased the concentration of the inorganic N compounds (NH 4 + , NO 3 − and NO 2 − ) that resulted in high coral mortality. The presence of the live rock remarkably reduced the concentrations and sustained a high coral photosynthetic activity. We detected the functional genes amoA and nirS within the live rock, suggesting the occurrence of both nitrifying and denitrifying bacteria. These results support the idea that “live rock” is an effective biofilter that can maintain water quality suitable for reef-building corals.