The paper discusses using Lake Baikal as a site for testing a near-surface TEM system. The water column of Lake Baikal forms a natural geoelectric model with precisely known parameters. Because of this, it has been possible to identify and assess the differences between the transient voltage responses measured with different arrays, and the corresponding modeled ones. It follows, from the field experiments conducted that the smaller the transmitter loop employed (central loop mode) the greater the difference between measured and modeled TEM responses. Since the geoelectrical model is known, this difference gives an objective assessment of the effect that the TEM system has on the overall measured response. It is notable that measured and calculated responses coincide when TEM soundings are done using separate loops (loop-loop mode).