A microfluidic surface trap was developed for capturing pH-sensitive nanoparticles via a photoinitiated proton-releasing reaction of o-nitrobenzaldehyde (o-NBA) that reduces the solution pH in microchannels. The surface trap and nanoparticles were both modified with a pH responsive polymer-poly(N-isorpopylacylamide-co-propylacrylic acid), P(NIPAAm-co-PAA). The o-NBA-coated microchannel walls demonstrated rapid proton release upon UV light irradiation, allowing the buffered solution pH in the microchannel to decrease from 7.4 to 4.5 in 60 s. The low solution pH switched the polymer modified surfaces to be more hydrophobic, which enabled the capture of the pH sensitive nanobeads onto the trap. When a photomask was utilized to limit the UV irradiation to a specific channel region, we were able to restrict the particle separation to only the exposed region. Via control of the UV irradiation, this technique enables not only prompt pH changes within the channel but also the capture of target molecules at specific channel locations.