The invertebrate indices for assessing water quality have not been widely developed in tropical regions where invertebrate diversity is generally high and severe water quality degradation is ongoing. We compared the applicability of six existing invertebrate indices using the dataset from 23 Indonesian streams and developed a new index by modifying an existing one using Threshold Indicator Taxa Analysis (TITAN). Analyses using general linear models (GLMs) revealed that among the six existing indices, the biological monitoring working party (BMWP)-based scoring system for Thailand streams (BMWP THAI) exhibited the strongest negative relationship with phosphate (PO4-P) concentration, a proxy for stream water quality. Based on the results of TITAN, five taxa were added to develop a modified invertebrate index, namely BMWP IDN, by assigning taxon scores in accordance with the responses to the water quality gradient. The relationship between the BMWP IDN and PO4-P concentration was found to be stronger than any of the existing invertebrate indices, indicating the superiority of the new index. Therefore, the extraction of uncovered sensitive taxa was important for modifying the existing index, and this study can contribute to improving the invertebrate index for assessing water quality of Indonesian streams.