Ancient reliefs in temple can provide information of past ecosystem along with biodiversity including Makara relief representing crocodile figure. In here, this study aims to identify and model the population of freshwater Crocodylus siamensis as portrayed in reliefs in 6 temples. The result shows that the crocodile reliefs in temples were having similar pattern to the freshwater Crocodylus siamensis fossils in term of locality. The temples and the fossils were located in the inland and near the rivers. While the temple locality patterns were in contrast to the locations where extant saltwater Crocodylus porosus has occurred. These contradictions strengthen the possibility that the crocodile portrayed in reliefs was made based on the C. siamensis occurrences. Based on the analysis, it is estimated that the C. siamensis once has occupied river and wetland in Java and its presence has been recorded in the reliefs. This occurrence at least happened from 1280 to 700 BC. From assessments of habitats near the temples using ᴪ AIC, most surrounding habitats have high detection probability and occupancy for C. siamensis from ᴪ 0.500 (95%CI:0.058-0.941). to ᴪ 1.000 (95%CI:0.000-1.000).