The consequences of global change on marine biota, particularly the interactions between human impacts and warming, are not well understood. An increasing frequency of extreme weather events will lead to pronounced short-term fluctuations in environmental parameters such as temperature, salinity and sedimentation in coastal ecosystems. At the same time, human populations are growing and coastal waters are increasingly loaded with nutrients and heavy metals. Direct effects of and interactions among these stressors will presumably alter the structure and functioning of ecosystems with negative consequences for the economical and social systems that depend upon them. In this context, we investigated the stress tolerance of populations of the Indopacific green mussel (Perna viridis, Linn. 1758) stemming from two coastal locations in West Java. P. viridis is a habitat forming species and can determine the composition of benthic assemblages in these systems. The two study sites differ in their abiotic conditions: Jakarta Bay is highly impacted by organic matter input and pollution, while Tanjung Lesung at the Sunda Strait represents a benign environment with low turbidity and almost no pollution. In laboratory experiments, we determined the mean tolerance of the two populations towards reduced salinity by 13 and 18 units, by measuring fluctuations in oxygen consumption and survival rates. Our results reveal that under reduced ambient salinity both responses were significantly different between populations. Mussels stemming from Jakarta Bay showed no mortality under reduced salinity levels within 21 days, whereas individuals from the benign site exhibited a mortality of 50 % at 15 psu and 20 % at 20 psu, respectively. Furthermore, the deviation in oxygen consumption under salinity stress from the normal performance was significantly smaller in mussels from Jakarta Bay than in mussels from Tanjung Lesung. Significant differences in survival and metabolic rates in the face of salinity stress suggest that the origin of a population contributes substantially to its tolerance towards increasing environmental stress. We discuss possible mechanisms that could underlie these differences in stress tolerance of two populations stemming from different coastal habitats.