Human activities in Jakarta City, Indonesia, produce huge quantities of litter, much of which is dumped in mangrove habitats along the coast of Jakarta Bay. We identified three mangrove sites that contained no litter to varying amounts of litter and assessed its effect on the bird communities that are associate with those mangroves. We conducted this survey to determine how many birds are living with litter, and what sort of litter it is, and its impact on bird species during October–November 2020. The study sites were Arboretum Muara Angke (AMA), Angke-Kapuk Protection Forest, (Hutan Lindung Angke-Kapuk, HLAK), and Angke-Kapuk Nature Recreation Park (Taman Wisata Alam Angke-Kapuk, TWAAK). We also calculated the Index of Waterbird Community Integrity (IWCI) at each site and determined its relationship to litter. This index has been used previously to study the impact of anthropogenic disturbances. Litter identified in the study areas mostly consisted of plastic, followed by processed wood and rubber. Most of the litter was stranded suggesting that the mangrove roots retain litter. Of the 28 species co-occurring with litter, 10 were waterbirds. Only two species, Oriental darter (A. melanogaster) and Milky stork (M. cinerea), were never present where there was litter, showing a significant negative correlation with litter. The IWCI was highest in AMA, followed by TWAAK and HLAK. Litter also has no correlation with the IWCI, but the IWCI tended to be lower wherever litter was found in higher quantities. When monitor regularly, the decreasing values of IWCI would be useful as an alarm for an improvement in the litter management by considering the different types of mangroves based on hydrological conditions. At the end, the management activities of mangrove as part of Ramsar and litter management should be integrated.