By monitoring changes in electrokinetic parameters, the streaming potential technique has been used as a method of characterizing heterogeneous surfaces, for example, due to protein adsorption. In general it is assumed that the change in the streaming potential is proportional to the degree of heterogeneity. In this study a simple model of the electrokinetic flow through heterogeneous slit channels has been developed with the goal of comparing the streaming potential and streaming current techniques and determining under what conditions the aforementioned proportionality assumption will produce erroneous results. The flow simulations have shown that, when the streaming potential induces significant flow impedance, a severe deviation from the linear assumption is observed. Since streaming current measurements are unaffected by electrokinetic flow effects, more consistent results are predicted and they are preferred for measurements made in small channels. Additionally it has been shown that the distribution of the heterogeneous coverage has a negligible effect on both the streaming potential and the streaming current in cases where the double-layer overlap is not significant,