The Citarum River, renowned as one of the most polluted waterways globally, traverses a basin exhibiting an urban–rural gradient and is inundated with diverse industrial activities, known to be significant contributors to its pollution levels. This study aims to evaluate the ecological health of the Upper Citarum watershed's industrial zones by utilizing macroinvertebrates as bioindicators. Throughout our investigation, we found that industrial sectors, particularly textiles, were closely linked to deteriorating water quality. This decline manifested in an increase in tolerant taxa and a decrease in sensitive ones. Such trends corresponded with escalating pollution index and low biomonitoring scores, indicating not only a decline in water quality but also significant sedimentation. Notably, Tubifex sp. emerged as the predominant organism in the Upper Citarum watershed, especially prevalent in textile and mixed industrial areas, accounting for 79% of the dissimilarity across all stations. However, this organism was conspicuously absent in pharmaceutical industry site. This absence resulted in significant differences in community composition compared to other industrial stations, as confirmed by both the analysis of similarities and the canonical correspondence analysis (CCA) graph. The separation of pharmaceutical industry sites from others in the CCA graph underscores distinct pollution and ecological statuses, primarily reflected to variations in the benthic macroinvertebrate community. Our study underscores the detrimental impact of industrial activities on the water quality of the Citarum River, urging future research to delve into the concealed risks posed by pharmaceutical waste. It emphasizes the urgent need for stringent pollution control and management strategies in this vital waterway.