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Detection of trace carbon monoxide (CO) dissolved in an aqueous phase is key for monitoring and optimizing biological and chemical gas conversions. So far, irrespective of the nonequilibrium nature of these conversion processes, because of low water solubility of CO, such detection has been performed indirectly, under the assumption of thermodynamic equilibrium, by the combination of chromatographic measurement of relatively abundant CO in a gas phase and Henry's law. Direct and sensitive detection of dissolved CO under nonequilibrium has not been explored yet. Here, we report the direct, ultrasensitive, and real-time monitoring of nonequilibrium dynamics of CO in an aqueous phase during biochemical conversions by devising miniaturized fluidic reactors with built-in CO-specific optical probes via surface-enhanced Raman spectroscopy. As the sensitive and selective probes, we fabricate ligand-free Au@Pd core-shell nanoparticle monolayers to maximize the Raman signal of single CO in the aqueous phase. We confirm that under equilibrium conditions, aqueous and gaseous CO concentrations estimated by our method are in good agreement with those measured directly and indirectly by gas chromatography (GC). We show that our probe can detect the aqueous CO concentrations as low as ca. 0.01% with high signal reproducibility, which is 200-fold more sensitive than that achieved by infrared spectroscopy. Finally, we successfully observe the nonequilibrium dynamics of the aqueous CO during biochemical reactions, which cannot be sensed by other detection methods including even indirect measurement by GC. We anticipate that our method can be widely applied not only for monitoring of biochemical gas reactions on multiple scales from a large reactor to a single-molecule level but also for molecular imaging of biological systems.