Real surfaces are typically heterogeneous, and microchannels with heterogeneous surfaces are commonly found due to fabrication defects, material impurities, and chemical adsorption from solution. Such surface heterogeneity causes a nonuniform surface potential along the microchannel. Other than surface heterogeneity, one could also pattern the various surface potentials along the microchannels. To understand how such variations affect electrokinetic flow, we proposed a model to describe its behavior in circular microchannels with nonuniform surface potentials. Unlike other models, we considered the continuities of flow rate and electric current simultaneously. These requirements cause a nonuniform electric field distribution and pressure gradient along the channel for both pressure-driven flow (streaming potential) and electric-field-driven flow (electroosmosis). The induced nonuniform pressure and electric field influence the electrokinetic flow in terms of the velocity profile, the flow rate, and the streaming potential.