The use of UV/ozone surface treatments for achieving low temperature bonds between PMMA and COC microfluidic substrates is evaluated. Low temperature bond strengths, approaching those of native polymer substrates bonded above their glass transition temperatures, are demonstrated for both thermoplastics. To evaluate the effects of the UV/O3 surface treatment on the operation of bonded microfluidic devices, the relationship between UV/O3 exposure and polymer hydrophilicity and surface chemistry are measured. Post-treatment surface chemistry is evaluated by XPS (X-ray photoelectron spectroscopy) analysis, and the stability of the treated surfaces following solvent exposure is reported. Electroosmotic flow within fabricated microchannels with modified wall surfaces is also characterized. Overall, UV/O3 treatment is found to enable strong low temperature bonds between thermoplastic microfluidic substrates using a simple, low cost, and high throughput fabrication technology.