Bivalve mollusks from the cooling reservoirs of fuel power plants (PP) are acclimated to the chronic heating and chemical pollution. We investigated stress responses of the mussels from these ponds to determine their tolerance to novel environmental pollutant, zinc oxide nanoparticles (nZnO). Male Unio tumidus from the reservoirs of Dobrotvir and Burschtyn PPs (DPP and BPP), Ukraine were exposed for 14 days to nZnO (3.1 μM), Zn²⁺ (3.1 μM) at 18 °C, elevated temperature (T, 25 °C), or nZnO at 25 °C (nZnO + T). Control groups were held at 18 °C. Zn-containing exposures resulted in the elevated concentrations of total and Zn-bound metallothionein (MT and Zn-MT) in the digestive gland, an increase in the levels of non-metalated MT (up to 5 times) and alkali-labile phosphates and lysosomal membrane destabilization in hemocytes. A common signature of nZnO exposures was modulation of the multixenobiotic-resistance protein activity (a decrease in the digestive gland and increase in the gills). The origin of population strongly affected the cellular stress responses of mussels. DPP-mussels showed depletion of caspase-3 in the digestive gland and up-regulation of HSP70, HSP72 and HSP60 levels in the gill during most exposures, whereas in the BPP-mussels caspase-3 was up-regulated and HSPs either downregulated or maintained stable. BPP-mussels were less adapted to heating shown by a glutathione depletion at elevated temperature (25 °C). Comparison with the earlier studies on mussels from pristine habitats show that an integrative ‘eco-exposome’-based approach is useful for the forecast of the biological responses to novel adverse effects on aquatic organisms.