Amperometric techniques are commonly used in lab-ona- chip systems to sense various blood gas analytes such as H+, CO2, O2, etc. In the present study, a microchip-based amperometric biosensor, being developed as a part of plastic-based structurally programmable microfluidic chip for clinical diagnostics at University of Cincinnati, is analyzed. For accurate modeling of electrokinetic transport and detection of various electroactive species, two levels of modeling are coupled: (i) fluid flow and transport of analytes and (ii) electrochemical surface reactions. In the present work, we have coupled the electrokinetic transport module [1][2] with electrochemical surface reaction solver. A detailed analysis of the system at the diffusion limit reveals that although the temperature variations are insignificant, the measured signal varies significantly due to Joule heating. An interesting phenomenon of increased sensitivity due to electrode-edge effect, caused by singularity at electrode edges, is also be observed and discussed.