A fuel cell system includes a fuel cell module comprising an anode section and a cathode section, a water gas shift reactor (WGSR) configured to receive an anode exhaust stream including carbon monoxide and steam and to output a WGSR exhaust stream comprising carbon dioxide and hydrogen, a condenser configured to receive the WGSR exhaust stream, to condense water in the WGSR exhaust stream, and to output a condensed water stream and a dried gas stream, a gas separation assembly configured to separate the dried gas stream into (i) a carbon dioxide stream comprising carbon dioxide and (ii) an output gas stream, and a cooling vessel coupled to the WGSR. The cooling vessel is configured to receive at least a portion of the condensed water and the carbon dioxide stream, to vaporize the condensed water stream using heat from the WGSR, and to output a humidified carbon dioxide stream.