An anaerobic digestion effluent (ADE) from the filtration facility of an anaerobic digestion process in a sewage treatment plant was used to cultivate the halophilic oil-producing microalga Chiorella sp. strain JPCC 0782. Secondary treated sewage (STS) was used as a dilution medium (ADE/STS) to avoid growth inhibition caused by high ADE ammonium nitrogen content. Chiorella sp. grew and produced lipids in the sterilized ADE/STS with 3.6 mM-14.4mM of the initial ammonium nitrogen concentration, thereby confirming the usability of ADE/STS as an algal medium. Although the microalga grew in the unsterilized ADE/STS in the raceway pond, ciliates also grew, resulting in consumption of the microalga biomass produced. Because the ciliates in the ADE/STS were inactivated at 10 psu, the salinity of ADE/STS was adjusted from 0.84 psu to 10 psu by adding seawater. We also demonstrated that adjusting salinity by adding seawater is a promising way to inactivate ciliates appearing in ADE/STS to prevent algal pond crash.