Fast pyrolysis and catalytic fast pyrolysis (CFP) of biomass produce a liquid product stream comprised of various classes of organic compounds having different molecule size and polarity. This liquid, either spontaneously in the case of catalytic fast pyrolysis or by water addition for the non-catalytic process separates into a non-polar organic-rich fraction and a highly polar water-rich fraction. The organic fraction can be used as a blendstock or feedstock for further processing in a refinery while, in the CFP process design, the aqueous phase is currently sent to wastewater treatment, which results in a loss of residual biogenic carbon present in this stream. Our work focuses on the catalytic conversion of the biogenic carbon in pyrolysis aqueous phase streams to produce hydrocarbons using a vertical micro-reactor coupled to a molecular beam mass spectrometer (MBMS). Furthermore, the MBMS provides real-time analysis of products while also tracking catalyst deactivation. The catalyst used in this work was HZSM-5, which upgraded the oxygenated organics in the aqueous fraction to fuels comprising small olefins and aromatic hydrocarbons. During processing the aqueous bio-oil fraction the HZSM-5 catalyst exhibited higher activity and coke resistance than those observed in similar experiments using biomass or whole bio-oils. Reduced coking is likely due to ejection of coke precursors from the catalyst pores that was enhanced by excess process water available for steam stripping. The water reacted with coke precursors to form phenol, methylated phenols, naphthol, and methylated naphthols. Conversion data shows that up to 40 wt% of the carbon in the feed stream is recovered as hydrocarbons.