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Rainfall parameter has been widely used as early warning criterion for sediment disaster. It is also used as the threshold in Mount Merapi, Central Java Province, Indonesia for mitigating lahar which is frequently induced by high rainfall intensity. The rainfall threshold called critical line was developed by correlation of two rainfall indices, namely short term rainfall index and long term rainfall index. Several methods for identifying those two rainfall indices was proposed by previous researchers. This research is aimed to compare the implementation of different rainfall indices by the means of distributed rainfall runoff model. Rainfall runoff model is capable to perform the relationship between rainfall and runoff considering the heterogeneity of a basin and estimate temporal distribution of flow depth and discharge. Based on the results, short term rainfall index and long term rainfall index represented by effective rainfall with 6 hours half-life and 1.5 hours half-life, respectively seemed to have better correlation to simulation results. From this research, it can be concluded that comprehensivee analysis to determine the best rainfall index can be achieved by the utilization of distributed rainfall runoff model.