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Emerging chemical contaminants [e.g. toxic metals speciation, flame retardants (FRs) and perfluorinated compounds (PFCs), among others], that have not been historically recognized as pollutants nor their toxicological hazards, are increasingly more present in the marine environment. Furthermore, the effects of environmental conditions (e.g. temperature and pH) on bioaccumulation and elimination mechanisms of these emerging contaminants in marine biota have been poorly studied until now. In this context, the aim of this study was to assess, for the first time, the effect of warmer seawater temperatures (Δ = + 4 °C) and lower pH levels (Δ = − 0.4 pH units), acting alone or combined, on the bioaccumulation and elimination of emerging FRs (dechloranes 602, 603 and 604, and TBBPA), inorganic arsenic (iAs), and PFCs (PFOA and PFOS) in two estuarine bivalve species (Mytilus galloprovincialis and Ruditapes philippinarum). Overall, results showed that warming alone or combined with acidification promoted the bioaccumulation of some compounds (i.e. dechloranes 602, 604, TBBPA), but also facilitated the elimination of others (i.e. iAs, TBBPA). Similarly, lower pH also resulted in higher levels of dechloranes, as well as enhanced iAs, PFOA and PFOS elimination. Data also suggests that, when both abiotic stressors are combined, bivalves' capacity to accumulate contaminants may be time-dependent, considering significantly drastic increase observed with Dec 602 and TBBPA, during the last 10 days of exposure, when compared to reference conditions. Such changes in contaminants' bioaccumulation/elimination patterns also suggest a potential increase of human health risks of some compounds, if the climate continues changing as forecasted. Therefore, this first study pointed out the urgent need for further research on the effects of abiotic conditions on emerging contaminants kinetics, to adequately estimate the potential toxicological hazards associated to these compounds and develop recommendations/regulations for their presence in seafood, considering the prevailing environmental conditions expected in tomorrow's ocean.Temperature and pH effects on emerging contaminants' bioaccumulation were assessed.Increased temperature promoted the bioaccumulation of Dec 602, Dec 604 and TBBPA.Lower pH increased Dec's bioaccumulation, but also iAs and PFCs' elimination.Human exposure to some compounds may increase with climate change.