A total of 25 sediment samples from surrounding Berau Delta, East Kalimantan have been used for microfaunal study. It is found some abnormal shells of ostracoda, foraminifera and other forms with darkish shells (black, dark green and dark brown). These forms were analyzed using SEM-Energy Dispersive X-ray spectroscopy (EDX or EDS) to know their chemical composition. The result shows that these abnormal forms composed of CaO, SiO2, C, FeO, Al2O3, K2O, and small amount of Na2O and Cl. They may derive from different sources: CaO and MgO from neutralized component during the environmental management to handle the Acid Mine Drainage (AMD). The other components may derive from coal ash during combustion process or other activities. From this result, the small amount (less than 5%) of abnormal shells may be used as early warning indicator of environmental changes in the study area