Water pollution and its impacts on ecosystems in Jakarta Bay have been extensively studied over the years. Muara Angke is known anecdotally as one of the most heavily polluted parts of Jakarta Bay. In the context of the ongoing debate regarding contamination in the area, we present data on the concentration of metals in green mussels Perna viridis, one of the most popular edible commodities in Jakarta Bay. Histological examination of P. viridis gonads was also performed to demonstrate the direct effects of possible contamination on reproduction in this organism. The concentration of arsenic (As), copper (Cu), nickel (Ni), zinc (Zn), and mercury (Hg) exceeded the upper limits of heavy metal contents in marine biota, whilst only As exceeded the maximum limits of heavy metal contents in processed food, both limits set by Indonesian government. Although the histological observation of gonad tissue after being stained with hematoxylin and eosin revealed some pathologies, high contents of metals in mussels collected in Muara Angke seemed not to affect their reproduction. Ecologically, direct impacts on the tissue of P. viridis will provide vital information needed to predict the health of the species in Muara Angke and the sustainability of the population.