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Hydrothermal conversion (HC) is a promising thermochemical technology to produce biofuels and bioproducts from biomass. However, the disposal of HC aqueous product (HC-AP) is one of the biggest challenges. This research investigated a new biological method using a marine protist, Thraustochytrium striatum to treat HC-AP from hydrothermal carbonization of municipal solid waste. A full factorial experiment was carried out to examine the effects of operation conditions on HC-AP treatment regarding cell growth, cellular lipid accumulation, and removals of total organic carbon (TOC)/total nitrogen (TN)/total phosphorus (TP)/recalcitrant compounds. Among four factors, only dilution rate and nitrogen concentration had significant effects on all responses, while salinity and pH were insignificant. Under the optimum conditions, T. striatum achieved 1.27 g/L dry cell mass and 14 % cellular lipid content while removing 82 % TOC, 53 % TN, 94 % TP, and ∼89 % refractory compounds. This research offers a new biological platform for HC-AP treatment and valorization.