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Abstract Pharmaceutically active compounds have been considered contaminants of emerging concern, in response to evidence that these substances may adversely affect non-target organisms. The pharmaceutical metformin is the most commonly prescribed anti-diabetes medicine throughout the world. Metformin has been detected in numerous freshwater systems as well as in seawater at a number of sites around the world over the last few years, but has never been reported in the Indonesian capital city Jakarta. Several recent studies have highlighted various ecotoxicological effects of this medicine on aquatic organisms. Here we report the first evidence of metformin’s presence in Jakarta waters. Samples from the Angke river, one of the main rivers in Jakarta, were collected from six sites. Metformin was detected at three sites in concentrations ranging from 27 ng/L to 414 ng/L. Metformin is one of the most detected APIs (active pharmaceutical ingredients) in aquatic environments worldwide, and there is increasing concern regarding its impact on the health of wildlife and humans. However, this is the first report of metformin contamination in Jakarta waters, adding to the evidence of potentially increased pollution with pharmaceuticals, as noted in our previous studies. With no natural degradation processes, these chemical compounds can be easily reintroduced to the food chain and impact human health.